100% OoT RTA Route as of 8/1/2012 : 

100% RTA:
Sword
Pause (1) and equip it. Savewarp.

WESS Escape
WESS to kak
Cucco collection
Get bottle
Navi Dive to BOTW
Get deku stick
Get Key
Open Door
Like-Like Room
Get Hylian Shield
GS in Like-Like Room [GS #1]
Get Deku Shield
Back through crawlspace
Actor glitch
Pause (2) and equip shield
Dead hand
LoT
Buffer clip to high water
Chus
Pause (3) and Savewarp

Market before dark
Side GS [GS #2]
Castle
Malon
Pause (4) and equip chus/egg
Damage from GS and [GS #3]
Wake Talon
Damage boost to ledge [9 Chu]
Zelda
CS skip [8 Chu]
Dot Skip
Adult
Pause (5) and Savewarp

Kakariko
Egg
Graveyard
Hookshot
Pause (6) and equip hookshot/chus/ocarina
ISG chu slide [7 Chu]
Hover boots
Pause (7) and equip hookshot/egg/ocarina. Savewarp

Sun's Song
Grave HP [HP #1]
Kakariko
Song of Storms and HP [HP #2]
Sun's Song warp to door
Wake Talon
Cojiro
DMT
DC
Pause (8) and equip hookshot/chus/ocarina. Equip hoverboots.
Chu Wall [6 Chu]
Switch
Pause (9) and take hover boots off
Chu staircase [5 Chu]
Chu Boost to GS in alcove [4 Chu][GS #4]
Pause (10) and remove hoverboots
GS on vines [GS #5]
Bombs [20 B]
Pause (11) and equip hookshot/bottle/bombs
Light Eyes [18 B]
Jump down
ISG and bomb wall [17 B][16 B]
Hover to GS [9 B][GS #6]
Utility Bomb [8 B]
Bomb wall [7 B]
Another GS [GS #7]
Head to back
Bomb from pot [12 B]
Bomb wall [11 B]
GS in back [GS #8]
Pause (12) and equip hoverboots
Catch a fairy
Hoverboots + drop fairy on switch
Pause (13) and equip hookshot/ocarina/bombs. Take off hoverboots
Run to door
Bomb floor [9 B]
KD + HC + Ruby [7 B]
GS behind hole [6 B][GS #9]
Blow up rock [5 B]
Sun's for dark
GS behind red rock [GS #10]
Bomb to magic [4 B]
Go for quick magic
Pause (14) and equip bottle over ocarina
Get bomb chest in grotto [20 B]
Get fish in grotto
Pause (15) and equip ocarina over bottle. Equip Hoverboots
Go in Goron City
Pause (15) and take off hoverboots
Come out
Damage buffer [18 B]
Bolero CS Skip [17 B]
Utility Bomb [16 B]
Goron City
GS on platform [GS #11]
LW warp (0.5 health if bold) [15 B]
Pause (16) and equip hookshot/bombs/chus
Mido skip
Forest stage
Chu GS, hookshot to get it [3 Chu][GS #12]
SFM
GJ over maze [14 B]
GS on right wall [GS #13]
Pause (17) and equip hookshot/ocarina/bombs
Minuet CS skip [13 B]
Utility Bomb [12 B]
Play Minuet
Pause (18) and equip hookshot/fish/bomb
Enter Forest
Key and GS first room [GS #14]
Bottle trick to basement [GS #15]
Back to top
Beat Stalfos for key #2
Back to main room
Clip OoB to avoid SoT Block
Megajump (Pause (19) and equip hover boots) [11 B]
GS to the right [GS #16]
Scale block room [10 B][9 B]
Pause (20) and take off boots
Stalfos
Take Damage from Stalfos if it works out
Bow
BK skip from Bow Room [7 B][6 B]
Pause (21) equip hover boots
Pause (22) take them off. Equip Bow/Fish/Bombs
ISG PG and go for bow strats [5 B]
Utility Bomb [4 B]
Defeat PG
Medallion cs skip with bomb [3 B]
Reverse Meadow
Get lost
Bomb drop from grass [8 B]
Tree GS [GS #17]
Megajump to ledge [7 B]
Pause (23) and equip hover boots
Pause (24) and take them off. Equip hookshot/bow/bombs
Enter Deku
GET DEKU NUTS !!!!
Slingshot
Compass Room GS [GS #18]
Break web
Torch both webs, get both basement GS [GS #19][GS #20]
231 Room, damage to 0.5 hearts from baba and fall damage if needed
Pause (25) and equip deku nuts/fish/bombs
ISG Kill Gohma
Emerald cs skip ww to DC [6 B]
Utility Bomb [5 B]
Superslide OoB Back to deku (or death if it fails) [4 B]
Pause (26) and equip hookshot/bow/bombs
Loop around Deku Basement as adult
Back room GS [GS #21][3 B]
Pause (27) and equip hookshot/ocarina/cojiro. Savewarp

Get HC in Deku and enter blue warp
Bomb drop from grass if needed [5 B at least here]
Lost Woods
Exchange Cojiro for Odd Mush
To Goron City
DMT
GS in Red Rock [GS #22]
HP above DC [HP #3]
House guy HP [HP #4]
Odd Potion
Pause (28) and equip hookshot/ocarina/bombs. Savewarp

Recoil DoT Skip (Pause (29) to equip hoverboots and (30) to take them off)
Skip Prelude
Recoil Dot Skip (Pause (31-32) for hoverboots and stuff)
Return Master Sword
Pause (33) and equip ocarina/slingshot/chus
Bolero
ISG off soil
2 slingshot chu hovers [2 Chu][1 Chu]
Pause (34) and equip deku stick/ocarina/bombs
2 Pause buffered bomb hovers [4 B][3 B]
Double Magic
Up to box GS [GS #23]
HP in climbable wall [HP #5]
Reset room
Goron City
Pause (35) and equip deku stick/fish/bombs
Light torches
Win HP from pot [HP #6][2 B]
30 Bomb bag [30 B]
Past boulders and shit [25 B]
GS in back [GS #24]
Dump fish, get bugs
Out of GC from top
GS from soil [GS #25][24 B]
Pause (36) and equip letter/ocarina/bombs
Give Letter to guard
Play prelude
Get Keaton Mask
SS to kak [23 B]
Sun's Song for dark
Show guard mask
2 upper Kak GS [GS #26][GS #27]
Sun's for day
HESS to Hylia [22 B]
Pause (37) and equip bugs/ocarina/bombs
HP from Grotto [HP #7][90 R]
ISG off sign
Bomb hover over fence [21 B]
Hopefully get a bomb drop [26 B]
Utility bombs [23 B]
GS from soil and GS behind house (suns if needed) [GS #28][GS #29]
Superswim to GS on fire arrow platform [GS #30][22 B]
Superswim to Pond [21 B]
Gold scale first, HP from big fish [HP #8][70 R]
Set Scarecrow's song
Ruto's letter
ZD
Get stick and nuts
Pause (38) and equip stick/nut/bomb
Light torches [HP #9]
KZ Skip [20 B]
Jabu without fish
Bomb first switch [19 B]
Ruto
Jumpslash GS in basement [GS #31]
Boomerang 
Pause (39) and equip boomerang/bugs/bombs
Both GS in basement, use bomb if extra [GS #32][GS #33]
Pause (40) and Savewarp

Rang first switch
Megaflip to switch + OI [18 B]
Rang switch from bottom
Get GS on vines [GS #34]
Pause (41) and boomerang/nuts/stick
Barinade + HC + stone
Pause (42) and equip boomerang/ocarina/bombs
Sun's Song
GS on log [GS #35]
Superswim if extra bombs
GS from tree [GS #36]
Bomb to FW [17 B]
Get FW
Prelude
Sun's Song
Skull Mask
Hyrule Castle
Din's [16 B]
ISG for seam
SoS hole
Blow up wall [15 B]
GS [GS #37]
Bomb drop from pot [20 B]
Minuet
Saria's Song
Pause (43) and equip bugs/skull mask/bombs. Savewarp

Soft Soil GS in kokiri [GS #38]
Pause (44) and equip letter (to dupe)/skull mask/bombs
To Lost Woods
Superslide or GJ past owl [19 B]
Utility Bomb [18 B]
Soil GS [GS #39]
Show skull mask for stick upgrade
Pause (45) and equip bugs/skull mask/ocarina
Sun's Song to reset area
Play Saria's Song for Skull kid [HP #10]
Exchange mask
Soft Soil GS [GS #40]
Pause (46) and equip slingshot on empty C
Deku stick upgrade [50 R]
Sun's Song to warp
Slingshot upgrade
Ocarina game [55 R] [HP #11]
Sun's Song to warp
Pause (47) and equip boomerang/din's fire/bombs
Know it all bros GS [GS #41]
SS to Gerudo [15 B]
Red rock area and bomb hole [14 B]
Dins fire
Get GS in hole [GS #42]
Utility Bombs or use on GS [13 B][12 B]
Enter GV
Pause (48) and equip boomerang/bugs/bombs
Use Cucco for HP [HP #12]
Soil GS [GS #43]
Waterfall HP [HP #13]
OoB Water back to top
GS near waterfall [GS #44] (should be just turning dark)
Cucco Jump
GF
GTG
Pause (49) and equip boomerang/chus/bombs
Clip to ice arrow, if needed with bomb [11 B][0 Chu]
Pause (50) and equip boomerang/bugs/bombs. Savewarp

Gate skip
Wasteland [10 B][9 B - two superslide this one it's fairly critical]
ESS through if good angle
GS at bottom [GS #45]
Collosus
SS to Spirit [8 B]
Soil GS [GS #46]
Pause (51) and equip boomerang/ocarina/bombs
Get Requiem
Prelude
Get Spooky Mask
Zelda Flee CS
OoT
SoT
To Tree Grotto [7 B]
GS in grotto [GS #47]
Sun's for night, enter Kak
2 GS in Kak [GS #48][GS #49]
Navi Dive to well
Pause (52) and equip boomerang/deku stick/bombs
Left Key's, middle room GSes [GS #50][GS #51]
Pause (53) and equip bugs/sling/bombs. Savewarp

Goodies in House of GS [HP #14][10 Chu]
Last GS by house of GS [GS #52]
Superslide to graveyard if extra bombs
Get bomb drop from bushes [12 B]
Dampe's Grave Digging Tour [HP #15]
Soil GS [GS #53]
Shoot sling to kill GS across
Pause (54) and equip boomerang/ocarina/mask
GS on wall [GS #54]
Sun's for day
Mask
Prelude
Bunny Hood
Pause (55) and equip mask/ocarina/bombs
Sun's Song
SS to tree [11 B]
Bomb it [10 B]
Dive to HP [HP #16]
Runnerguy [500 R]
SS to Lon Lon [9 B]
Utility Bomb [8 B]
Pause (56) and equip sling/rang/bombs
Kill GS on wall with slingshot, get with boomerang [GS #55]
Tree GS [GS #56]
Superslide to stable [7 B]
GS on back of stable [GS #57]
Superslide to far wall [6 B]
Utility Bomb [5 B]
GS on wall, curse at the guays [GS #58]
Back HP [HP #17]
Pause (57) and equip LoT/ocarina/bombs
Make it day
SS to malon [4 B]
Utility Bomb [3 B]
Epona's Song
Bottle Game for milk
Prelude
Mask of Truth
Slingshot game
Sun's Song for night
Bombchu bowling [HP #18][40 B]
Richard HP [HP #19]
Buy 20 chus [30 Chu]
Treasure Chest Game [HP #20]
Pause (58) and equip MoT over LoT. Savewarp

Lost Woods
Superslide/GJ to skip owl [39 B]
Deku Nut upgrade
Backtrack to ZR warp
Pause (59) and equip boomerang over MoT
Dive to ZR
HP on ledge with rang [HP #21]
GS on ladder [GS #59]
Frog ocarina game for 2 HP [HP #22][HP #23]
A, left, right, down, left, right, down, A, down, A, down, right, left, A
HP on ledge down river [HP #24]
Buy 2 magic beans, ISG off bean seller
Pause (60) and equip bean/ocarina/bomb
Plant one
Bomb rocks [38 B]
GJ for tree GS and skip owl [GS #60][37 B]
Utility Bomb [36 B]
Bolero
ISG
Plant Bean
Pause (61) and equip bugs/chu/ocarina
Pause (62) and dupe milk
Soil GS [GS #61]
Chu hover to fire temple [29 Chu]
First key on left
Prelude
DoT Skip
Adult 2
You have Ocarina, Bombs, Hookshot.
Minuet
Pause (63) and equip bow/odd potion/bombs
Nut upgrade [35 B]
Get lost
Return to Lost Woods
Trade Potion for Saw
Pause (64) and equip hook/saw/bombs, equip hoverboots
To Lost Woods bridge
Pause (65) and take boots off
Exit to hyrule
SS to Lon Lon Ranch [34 B][33 B]
SS to GV-side fence [32 B][31 B]
Steal Epona [30 B][29 B][28 B]
Head to GV, getting poes 4+5 (http://www.zeldadungeon.net/Zelda05/Walkthrough/09/Map_BigPoeLocations.jpg)
Jump bridge with Epona
Trade Saw
Two GS on other side of bridge [GS #62][GS #63]
Make it dark if not
Middle stair, shoot guards
Entry in middle of Fortress
Guard #1
Guard #2
Pause (66) and equip hover boots. Equip hookshot/ocarina/bombs.
Hoverboots to Fortress Heart Piece [HP #25]
Pause (67) and take off hoverboots
GS on upper wall [GS #64]
Guard #3
Pause (68) and savewarp

Guard #4 for Gerudo Card
Sun's Song
Epona's Song
Archery for 40 Quiver and HP [HP #26]
Sun's Song again
SS across to target [27 B][26 B]
Utility Bombs [25 B][24 B]
GS on target [GS #65]
Pause (69) and equip hookshot/ocarina/broken goron sword
Bolero
Trade Broken sword for Prescription
Pause (70) and equip the big poes (leave ocarina). Savewarp

Deposit Poes
Hyrule
Epona
Two more Big Poes (1 and 9)
Zora's River
Ride Bean
Sun's Song for night
Enter Grotto
Pause (71) and equip hookshot/bottle/bombs
Dupe over deku nuts (Pause (72))
Get GS [GS #66]
Get 2nd GS [GS #67]
Hoverboost into ZD
Acute angle past KZ
Enter Ice Cavern
To spinning ice scythe room
Clip through red ice on right
Pause (72) and equip hookshot/bottle/bombs
Get blue fire
Get HP [HP #27][23 B]
Kill GS [GS #68]
Back to main room
Get GS [GS #69]
Melt red ice
Catch blue fire and get Silver Rupees [22 B][21 B][20 B]
Kill GS [GS #70]
Recoil boost through red ice [pause (73-74) and equip hookshot/ocarina/bombs]
White Wolfos
Buffer down to 0.5 hearts [20-15 B]
Iron Boots and Serenade CS Skip [14 B]

OoB Clip
Pause (75) and put on Iron boots to sink
Pause (76) to swim behind wall
GS on high ledge [GS #71]
Megaflip to HP on iceberg [HP #28][13 B]
Pause (77) and equip Iron Boots
HP at bottom [HP #29]
Pause (78) and take off Iron Boots. Equip hookshot/bluefire/prescription
Unfreeze KZ
Clip through him, get tunic and eyeball frog
GS in Domain [GS #72]
OoB to Hylia
Pause (79) and equip hookshot/ocarina/eyeball frog
Finish learning scarecrows
Bomb drop(s) from grass [18 B][23 B]
Roof HP [HP #30]
Lakeside Lab
Dive to bottom
Pause (80) and equip Iron Boots.
GS at bottom [GS #73]
Pause (81) and take them off
HP from lab guy [HP #31]
Eyedrops
Bolero timer trick
Up to biggoron
Trade, then Sun's x5 or 6
After last sun's, make it night
Biggoron's Sword
Play Serenade
Pause (82) and equip Iron Boots
Enter Water Temple
Pause (83) and take off Iron Boots
Go down to ruto via iron boots swim [Pause (84)]
Pause (85) and equip hover boots. Equip hookshot/bow/bombs. Equip BGS
Lower water level
Sidehop to middle level and get key behind bombable wall [22 B]
Go down and light torches for key in shellblade room
Main room, go to tunnel left of the one you just came from and blow bombable floor [21 B]
Go through water tunnel
Pause (86) to equip hookshot/bow/bombs
Get two bomb drops from pots [31 B]
Take damage to around 6 hearts
Get GS in the room at the end [GS #74]
Pause (87) and equip hover boots. Savewarp

Hover to ledge
Pause (88) and take off hovers
Pause (89) and hover boost to open upper left door [30 B]
ISG to get GS on the wall with hookshot [GS #75][29 B]
Go to dark link
Pause (90) and take hover boots off. Equip hookshot/bow/ocarina
Defeat Dark Link
Get longshot
Down to vortex room
Pause (91) and equip iron boots.
Get GS on the wall [GS #76]
Pause (92) and take off iron boots
Hit eye switch and get key from chest
Pause (93) and Savewarp

Jump down to middle floor on tower
Light torch to open door
Get GS at the top of the room [GS #77]
Back to main room
Jump straight down to the water passageway
Go to the room with tektites and boulders
Shoot GS w/ bow
Get GS from waterfall near boss key room door without climbing ledge [GS #78]
Pause (94) and equip ocarina/FW/bombs. Savewarp.

Superslide [28 B][27 B]
Pause (95) to equip hover boots, equip longshot/FW/bombs
Cast FW
Pause (96) and equip longshot/chus/bombs
BK SKip [26 B][25 B][26 Chu]
Utility Bombs [23 B]
Defeat Morpha w/ 0.5 hearts
Pause (97) and take off hover boots. Equip FW/fish/bombs
OI on blue warp
Death medallion CS Skip [22 B]
Warp to FW spot
Pause (98) and equip fish/chus/bombs. Equip hoverboots
BK SKip [21 B][20 B][23 Chu]
HC
OI Serenade with fish
Pause (99) and equip longshot/ocarina/bow
Sun's for night
Longshot GS in tree [GS #79]
Sun's for day
Shoot to Fire arrow
Scarecrow song, longshot to fire arrow
Bolero
Enter fire temple
Go in right door
Go to the left and save goron + key
Exit, play SoT and enter above room
Get GS near likelike [GS #80]
Pause (100) and equip longshot/FW/bombs
Back to large lava room
Cross the room to the other side (take lots of damage)
Save goron + key [19 B]
Go to next room and push block on fire spout to go up to next room
Pause (101) and equip hover boots
BGS clip through block
Pause (102) take off hover boots and jumpslash through to room
Press switch, get Key
Climb up ladder
Enter/Exit door to Fire wall room
Cast FW
Jump down and get GS [GS #81][18 B]
Get Key on bottom floor from Goron Jail Cell
Pause (103) and equip longshot/FW/ocarina and equip hoverboots. Savewarp

BGS clip through first room wall
Pause (104) and take off hover boots
GS in next room [GS #82]
Warp back
Cast again
Scarecrow song 
Hook up to him, get both GS in tower [GS #83][GS #84]
Warp with FW
Pause (105) and equip longshot/bow/bombs. Equip Master Sword
SS past fire maze room [17 B][16 B]
Blow up wall, get bomb drops from pots [26 B] and avoid the hearts
Flare Dancer, take damage if necessary
Bomb switch in next room [25 B]
Hammer
Damage to 5 hearts if needed [24 B]
Utility Bomb [23 B]
Pause (106) and equip longshot/hammer/bombs
Hammerslide BK skip [(Pause (107) for hoverboots)]
Pause (108) and take off hoverboots. Equip BGS. Equip fish/hammer/chus
1 cycle Volvagia with chu + fish strat
Medallion CS Skip WW to Forest
Pause (109) and equip longshot/bow/fish
Shoot eye
GS on right courtyard [GS #85]
GS on right by BK skip area [GS #86]
BK skip again
Get HC
Fish OI for Bolero
Cone HP [HP #32]
Goron City
Pause (110) and equip longshot/ocarina/bombs
Superslide [22 B]
Pause (111) and equip Iron Boots
Pause (112) and take them off
Buy Goron Tunic and Bombs if needed
Pause (113) and equip poes and ocarina. Savewarp

Drop Off Poes
Epona's Song
Get Poes 8-6-7
Try to Get HF glitch and requiem
Pause (114) and equip longshot/ocarina/bombs
Superslide to NL if you have the bombs
Bomb wall for NL [21 B]
NL
Pause (115) and equip longshot/bow/bombs
Go get GS tokens [GS #87][GS #88]
SS back to Spirit [20 B][19 B]
Kill guay
Pause (116) and equip hoverboots after set up. Equip longshot/chus/bombs
Hover to seam using chus/bombs [18 B][17 B]
Longshot SG chest
Pause (117) and equip longshot/FW/bombs
Enter, cast FW, leave
Hoverslide [Pause (118) and equip hoverboots] to platform HP [HP #35][16 B][15 B]
Enter Spirit
Pause (117) and equip longshot/Fire Arrow/bombs. Equip MS. Take off hoverboots.
Superslide to clip [16 B][15 B]
Pause (118) and equip hover boots
Pause buffer clip
GS on child side [GS #89]
Light torches with fire arrow and get key
Wallmaster reset
Pause (119) and equip hoverboots. Equip longshot/ocarina/bombs
Bombs from armos [20 B]
Silver Block skip with GJ [19 B]
Collect GS [GS #90]
Pause (120) and equip longshot/FW/bombs. Take off hoverboots.
Warp to FW
Cast again
Use key
GS wall [GS #91]
Warp to FW
Hoverslide [pause (121)] to mirror side [16 B][15 B]
Utility Bombs [13 B]
Mirror shield
Pause (122) and equip mirror shield and BGS. Take off hoverboots. longshot/ocarina/bombs
IK
4 armos room
Get bomb drop if needed [18 B]
Key
Moving wall room
BK
Mirror room [17 B]
Lower platform
Child side GS [GS #92]
Longshot chains
GS in main room [GS #93]
Nabooru and Twinrova
Pause (123) and equip 3 big poes. Savewarp

Deposit 3 poes
Hyrule field
Pause (124) and equip ocarina over bottle
Catch last 3 poes (3-2-10)
Go to kakariko
Nocturne
Pause (125) and equip longshot/ocarina/din's
Clip to archery
Play for 50 quiver
Clip through again
Longshot to house
Get GS above Impa's House [GS #94]
House HP [HP #34]
Play Nocturne
Open Shadow
Pause (126) and equip longshot/lens/FW
Truth Spinner first try
Pause (127) and take off hoverboots. Equip longshot/lens/bombs
Silver Rupee room
Get Key
Set FW
Bomb wall [16 B]
Main Room
GJ to avoid Navi [15 B]
To likelike room
Like-like clip for GS [GS #95]
Main room
Jump a few platforms
Superslide [14 B][13 B]
Pause (128) and equip hoverboots. Equip longshot/lens/FW
Silver Rupees
Get GS in lower Gate [GS #96]
Spike trick
Get key
Back to main room
Over invisible platforms
Pause (129) and take off hoverboots. Equip longshot/ocarina/FW
Key and GS [GS #97][11 B]
FW
JS gate trick
Get GS [GS #98]
Boat ride
Take lots of damage from stalfos (down to 1.5 hearts)
Set FW in room
Get GS in spinning skulls [GS #99]
Get BK
Warp with FW
Pause (130) and equip FW/ice arrow/bombs
Hoverslide across [10 B][9 B], pause (131 and 132) for hoverboots
Utility Bombs [6 B]
Cast FW in pre-boss room
Pause (133) and equip longshot/ice arrow/fish. Take off hoverboots
Fight Bongo with ice arrow
Shadow set up
Pause (134) and equip longshot/fish/FW. Take off goron tunic. Equip MS.
Medallion CS Skip
Warp to FW
Pause (135) and equip Hoverboots
HC
Pause (136) and equip longshot/bigpoe/bigpoe. Put on goron tunic for style. Equip BGS.
Blue warp
HP in box [HP #35]
Dampe's Grave
Get nuts back over fish
Race Dampe again for HP [HP #36] 
Pause (137) and equip 3 big poes. Savewarp

LA CS
Deliver Poes
Last bottle
Pause (138) and equip longshot/ocarina/bombs
To Ganon's 
SS to DD [4 B][3 B]
Recoil clip into fountain (Pause (139) and equip hoverboots)
Pause (140) and take off hoverboots
Kill last GS [GS #100]
Get Gold Gaunts w/ longshot
Reset room
Do trials skip [2 B][1 B][0 B]
Pause (141) and equip longshot/light arrows/bombs
Kill dorf
Castle escape
How about a kiss for luck
Pause (142) and equip master sword
Jumpslash, enter cutscene
Pause (143) and equip BGS
Crouch stab 3 hits
Master Sword back
Kill him
.done