Math rock is a pretty widely used term. Some of these bands will be more song structure oriented, and some are pretty much only for musicians into hearing other musicians do weird, albeit annoying, things with music. I will guarantee, however, that all of these bands employ compound rhythms, stop/start riffs, and odd-meter timing in their song writing. So here goes-
Shiner- Try "Lula Divinia". It's their masterpiece. "The Egg" is pretty damn amazing, too. Great, catchy songwriting that's the size of a steamroller.
Jawbox- "For Your Own Special Sweetheart". In a similar vein as Shiner, but poppier.
Burning Airlines- "Mission: Control!" Basically Jawbox, with a few members changed.
Ring, Cicada- "Good Morning, Mr. Good" From the jazz-rock school. I love these guys.
Table- "Table". Short lived Chicago band. Good luck finding this one. It's great though.
Dazzling Killmen- "Face of Collapse"- Noisy, jazzy, aggressive, stop/start stuff that's annoying and wonderful all at once.
Grand Ulena- Darin Gray from Dazzling Killmen's new band. These guys are just plain nuts. Their songs have a logic all their own. It sounds like chaos with sudden bursts of a song that comes together all at once. Not for the faint of heart. There's an amazing youtube video of these guys. Listen to the whole thing before you dismiss it.
Yowie- St. Louis folks in the vein of Grand Ulena. They use micrtonal tunings and also sound like controlled chaos. They lack the aggressiveness of a band like Grand Ulena, and sort of remind me of what it would sound like if circus clowns started a math-rock band.
Don Caballero- "American Don". Damon Che. 'Nuff said.
Seven Storey Mountain- "Dividing by Zero". Sort of in the Shiner, Jawbox vein.
The Casket Lottery- Past members of Coalesce go all emo with stop start songs and sudden timing and tempe changes.
31 knots- Defeintely in the jazz-rock vein. These guys are great.
Houston- Closest to Shiner, these guys write BIG riffs. They were a great live band.
Faraquet- "The View From This Tower". I know it's already been mentioned. I'm mentioning it twice, that's how good it is.
Hope that gets you started.