Death Cab for Cutie aren’t the studliest boys around, either. I can’t find a truly geeky picture right now, but watch their recent dvd and it’ll all become very clear.
Well, the Minutemen were very much geeks. Making their situation all the more humorous, they were heavily involved in the 1980s American underground punk scene. Try to imagine a couple of total dorks who play weird, experimental music getting spat on and kicked by angry skinheads and punks during a raucous concert. 
I vote for The Gothsicles.
Their lead singer wears a Nintendo Power Glove and a NES controller as a belt buckle on stage, and they do songs like “Konami Code” and “Devastator” (the latter being about Transformers). Very geeky.
Artichoke has a dedicated theremin player that actually works at the Jet Propulsion Lab. What’s more, they have an ongoing project called 26 Scientests that is an attempt to record a song about a scientest for every letter of the alphabet. They really sound good, too.
I think that this thread deserves mention of a nerdcore proponent.
What say we give a big shout out to MC Plus+! With titles like “End of File” and “Have to Code”, he brings the programming world to life in his def rhymes.
Yo yo yo, check out his album Algorhythms
How about Barcelona? Long time ago someone sent me the song “I Know the Password to Your Shell Account” which you can (legally) download here. I haven’t listened to other tracks yet, but here’s a quote from a review:
I present you with “The Darkest of the Hillside Thickets”. A band inspired almost entirely by H.P. Lovecraft. Geek-o-rama. :>>