Thrice have switched amps up quite a lot through their career, and we can almost see the progression of them as musicians through their amps. The Mesa Dual Rectifier days of old have ended (think "Illusion Of Safety"), and for the band, so has that scooped mid, generic metal sound we've heard thousands of times before (though the songs were never quite so nice from anyone else). Thrice look elsewhere for their "heavy" tones now: The fire EP was recorded (even the bass) mostly through Marshall JCM800 amps. These are powerhouse, fiery amps but they're a different kind of "heavy". Distinctly more clear, and more about power, tone and midrange than a Rectifier.
For main amps, Thrice have settled on other things. Teppei added a Fender '59 Bassman reissue to his setup not too long ago and apparently is loving it for the way it has its own character. Regardless of the guitar being played, you can tell for sure that it's a Bassman. This seems to be what Teppei is using the most now, and it was the only amp he had on the Conan set when they played Come All You Weary. For a stripped down Tele/Bassman demo check out the video of that performance. The result is one of my favorite tones I've heard from Thrice. Teppei has also been a fan of the classic Vox AC30s for the past couple years. These are also an unconventional amp for a band like Thrice. They were the choice amps for many rock guitarists in the 60s and 70s (notably the Beatles and Brian May), and have warm clean tones and the tubes will overdrive beautifully for creamy, tasteful drive. I imagine when he needs to go over the top live, his Turbo RAT will do the job. Notice how downsized this setup is from the stacks of Marshalls, Bogner Uberschalls and Mesas. The bottom line with tube amps is that you don't need a million watts in a live situation. Where 100 watts solid state would be just enough for a decent size gig, 100 watts of tube power would blow the house down. With the sound also being filtered through the PA- this really isn't needed.
In the summer of 2007, Dustin sold his JCM800 2205, Mesa Dual Rectifier and Mesa Boogie cabs, stating that it was time for a change. This change was his drifting further toward modeling equipment, namely Line 6. Currently (fitting in with the shift toward smaller amps) he is using 2 Line 6 Vetta II amps with 2 12" speakers. The Line 6 amps work perfectly with his Variax modded Nash Tele and new Line 6 pedalboard, allowing for more convincing modeling.
Eddie is, and has pretty much always been an Ampeg user. His powerful low end punch comes from an Ampeg SVT Classic Anniversary head paired with an SVT 8x10 cabinet. Maybe the 8x10 doesn't fit with the "less is more" approach of Teppei and Dustin, but bass is a different world and in a live situation a general rule is that the bass amps should have twice the wattage of the guitar amps.