It was mainly Jonny who used small amps during the recording of In Rainbows. That said, Thom did use some mid-sized combos like a Mesa Boogie Dual Rectifier Maverick 1x12 and a Selmer Truvoice TV12T during those sessions, which are a certainly a down-size from his Vox AC30. A photo showing both those combos is at the top of Thom’s amplifiers page. Ed mostly used mid-sized Fender combos, including a Fender Super-Sonic 112 combo.
The best place for more info is probably our article on Jonny’s scraping technique and clean tone on Nude. It dips deep into his setup on In Rainbows, and also explains the techniques that took advantage of the new (vintage) gear.
You can read more about one of those bits of gear, a rare Orpheum combo belonging to Nigel, in this post.
And try searching for “In Rainbows” on Jonny’s amplifier page, that lists all of his small amps from those sessions.
And of course, who can forget the Squier SP10! That’s doubtless the most affordable amp they’ve been seen playing.

Thom, Ed, and Jonny taking a tea break during the recording of In Rainbows (deadairspace). Presumably, they’re laughing at Nigel’s (?) decision to record the tiny, cheap Squier SP10 “practice amp” with a super-expensive vintage Neumann microphone.

Jonny re-arranging his pedals on the “first day back” at the studio in early-2007, during the recording of In Rainbows (deadairspace). Behind him are a bunch of amps including a 1953 Fender 5C1, a Squier SP10, a Fender Twin Reverb, a Vox AC30, a Selmer Truvoice TV12T, and others.