This thread was a great idea. Here's my $.02, even though a lot of them have been mentioned already:
Aesop Rock - check out anything by this guy
Sage Francis - like 90% of his stuff. Check out "Slow Down Gandhi", "Different"
Eyedea & Abilities - "Now"
Quannum Projects - "Jada's Revenge"
Immortal Technique - Probably should stear clear if you're a George Bush fan. Tracks you should get = "4th Branch", "Cause of Death", "Peruvian Cocaine"
Rob Sonic -Telicatessen cd is good, "Super Ball", "Strange Hammer"
Vordul Megilah - formerly of CanOx, "Spitamatic", "Blade"
Busdriver - some crazy stuff, chech out "Imaginary Places"
Tech N9ne - not exactly underground, but still doesn't get played on the radio. Get "This Ring", "Imma Tella", "The Grinch", to many others to list...
Swollen Members - "Fuel Injected", "Full Contact", "Lady Venom"
Spooks - "Deep Cuts", "Karma Hotel", "Sweet Revenge"
Promatic - "Do what I wanna"
Cap One - Not really thinking man's music, but it's fast and loud. "Chi Town's Finest", "Ride n Smoke"
Blackalicious - "A to G",
Andre Nickatina - "Ayo for Yayo", "Alligator Blood"
Don't forget Gorillaz, they're more than just "Clint Eastwood"
Hangar 18 - "Blown Bubble"
I'll stop now. Sorry to monopolize page 4.