Disclaimer: I don't have access to every 2006 live performance. There might be some interesting performances I haven't heard yet. This list will be updated when I do get to listen to them. Also it will be updated if after relistens change my mind.
15 STEP_
Aside to some slight structural and lyrical changes, it's pretty similar to its final form. These changes fade away in later 2006 performaces.
RECOMMENDED PERFORMANCES
(Debut) Copenhagen Night 1
Bonnaroo
Hummingbird Centre Toronto
Boston Night 2
Empress Ballroom Blackpool Night 2
Auditorium Theatre Chicago Night 2
B/ODYSNATCH ERS
I don't notice any differences aside from Ed's added backup vocals.
RECOMMENDED PERFORMANCES
(Debut) Copenhagen Night 1
Bonnaroo
Greek Theatre Los Angeles Night 2
Hummingbird Centre Toronto Night 2
Copenhagen Night 2
N_UD E
I don't notice any changes aside from possibly some different effects?
RECOMMENDED PERFORMANCES
(Debut) Copenhagen Night 1
Bonnaroo
Amsterdam (August)
Hummingbird Centre Toronto
Edinburgh Scotland
A/RPEGG_I
Weird Fishes/Arpeggi was still called Arpeggi at this time. The song doesn't start with drumming, it starts instead with the guitar, then the drums come in. For some reason I prefer this even if it barely matters. Also, it sounds a bit noisier than the one on In Rainbows.
RECOMMENDED PERFORMANCES
(2006 Debut, Acoustic) Koko (Thom & Jonny)
(Radiohead Debut) Copenhagen Night 2
Bonnaroo (my favourite Weird Fishes/Arpeggi performance I know)
Hummingbird Centre Toronto
Greek Theatre California Night 1
ALL I NEE/D
I'm pretty sure it has some extra twinkling chime noises at the beginning. It also has some important lyrical changes. Ex: "I'm a flash flood running through your ground floor/I am all the things that you choose to ignore."
RECOMMENDED PERFORMANCES
(Debut) Auditorium Theatre Chicago Night 2
Greek Theatre Los Angeles Night 1
Amsterdam (August)
HO/US E OF CARD_S
I don't notice many differences.
RECOMMENDED PERFORMANCES
(Debut) Copenhagen Night 1
Bonnaroo
Hummingbird Centre Toronto Night 2
Greek Theatre Los Angeles Night 2
O_PEN PIC K (JI GSAW FALLI_NG I/NTO PLAC_E)
One of the most exciting of the early In Rainbows versions in my opinion. It's more electric rather than acoustic. There's some extra arrangement changes as well. I prefer this version to the one on In Rainbows. Some of the performances of this song in 2006 are the best I've heard. I can't stress how much I prefer this song live, the released version sounds so much more lifeless in comparison.
RECOMMENDED PERFORMANCES
(Debut) Amsterdam (May)
Hammersmith Apollo Night 2 (Really great version)
Wolverhampton Night 2
Hummingbird Centre Toronto Night 1
Auditorium Theatre Chicago Night 1
VIDE OTA_PE
Probably the most different sounding early version. It's much brighter, energetic, more melodic instead of the solemn and skeletal one on the album. I love both a lot with some preference towards the 2006 version. But there's people who dislike the In Rainbows version and much prefer the 2006 version.
RECOMMENDED PERFORMANCES
(Debut) Hammersmith Apollo Night 1
Hammersmith Apollo Night 2
Bonnaroo
Auditorium Theatre Chicago Night 2
Greek Theatre Los Angeles Night 1
MSG New York Night 2
DOW_N IS THE NE/W UP_
It was only performed in 2006 and hasn't been played since (a shame).
RECOMMENDED PERFORMANCES
(Debut) Hummingbird Centre Toronto Night 2
Greek Theatre Los Angeles Night 1 (haha)
Auditorium Theatre Chicago Night 2
Greek Theatre Los Angeles Night 2
/GO SLO_WLY
The most clear change is the added drums. They give the song a grand atmosphere. They also make it sound a bit more like Thief by CAN, a song it was based off of. It's a really interesting touch that isn't in the released version.
RECOMMENDED PERFORMANCES
(Debut) Blackpool Night 2
Montreal Night 2
B/AN_GERS + MAS H
Lyrics are a bit different! "I want to thank you, thank you all." Fairly similar though.
RECOMMENDED PERFORMANCES
(Debut) Copenhagen Night 1
Hummingbird Centre Toronto Night 2
Boston Night 1
MSG Night 1 (??)
4 MI_NUTE WAR/NING
Another song that was exclusively performed in 2006. It has drums unlike the released version.
RECOMMENDED PERFORMANCES
(Debut) Copenhagen Night 1
Empress Ballroom Blackpool Night 2
SPOO_KS
Spooks! Fun 1 minute song that didn't show up on the album. Instead, it was developed and got used in a song Jonny did for the film Inherent Vice in 2014. It was exclusively performed in 2006
RECOMMENDED PERFORMANCES
(Debut) Copenhagen Night 1
Greek Theatre Los Angeles Night 2
Reckoner and Faust Arp were not played on the 2006 tour and were not performed earlier. Well, of course, Reckoner was played in 2001 but it sounds nothing like the one on In Rainbows. Also, Up On The Ladder was not played in 2006 despite it having already debuted in 2002.