I listen to Tortoise (great band) and most of their side projects too (Isotope 217, Chicago Underground Duo/Trio/Quartet, Brokeback etc. etc.) so hope I can shed some light on this...

unless you specifically hang out with the band or help engineer their sessions, I don't think you'll ever really know anything too specific about their methods (Tape Op interviewed John McIntire last month, you may want to check out that fine publication).

they use both live drums and beat boxes (of course)...I've seen them live, and they used a Slingerland kit and for the programmed stuff they used either a Roland MC-303 or MC-505 and possibly a sampler of some sort. on record, it's hard to say what is what, they are Pro Tools users and they surely must do a lot of editing and of course they do some heavy FX mutation to the drum sounds overall. if you go to the SOMA website I think there is a gear list that may shed some light on where some of the sounds come from (quite a bit of choice vintage synthesizers).

obviously on some of their more 'normal' material, you can pretty much figure out what's going on...IMO, some of the drum sounds they've achieved don't blow me away, but within the fabric of the song seem to do the trick.

Tortoise is one of the few bands that make me turn off the engineer side of my brain and let the music-lover side take over once again!
;)

OK Computer,
I think a few issues back 'Tape Op' featured Soma.
The studio has a truly massive collection of analog modular synths.
Also a 24 track analog 2 in. thingy, and pro tools/logic.

If your wondering about that chunky swooshy sort of sound like on the first cut of standards, the drums are being processed through an analog lowpass filter, or maybe you already knew that.
I think the sherman filterbank and mutronix mutator are both excellent analog filters.
The electrix filter factory is inexpensive, doesnt sound as good though.

If you want an analog beatbox, there's besides 909/808 the vermona drm-1 and jomox airbase 99. The mc 505 has some nice samples for a rom unit.
I think its the coolest thing since sliced bread though is machine drum, a physical modeling(cough cough, not just analog either) drum machine.
http://www.machinedrum.com

Also filterbank:
http://www.sherman.be

Now also we get to the modular synths, real analog modulars. I know the wiard modular was featured on the new tortoise album, and it made some strikingly beutiful appearances.
Ive really enjoyed some of tortoises and isotope's music!
They are tha bombz.