This might become a big list, but you asked for it
First and foremost: Roots & Black Thought, Public Enemy & Chuck D. Forget Tupac & Biggie, Black Thought and Chuck D are the greatest of all time.
Sabac Red, of former Non-Phixion fame. This guy is the best political rapper out there, period. Think Immortal Tech, but with a bit more variation in subject matter.
Revolution of the Mind. Waiting for the first album, but from what I've heard so far, it's going to be ridiculous.
Sage Francis. A true poet. Makes you really pay attention.
Rugged Intellect. Mad flow, I think that's all that needs to be said.
Xzibit. People usually don't take him seriously because he's famous, but he is one of the best, no other way of putting it. Heart of Man, At The Speed of Life, Carry the Weight etc.
Hus (& Libyus Creators). Jazz-hop. Chill.
Nieve & Cook. Same deal.
Promoe, of Looptroop fame. Occasionally conscious and deep (These Walls Don't Lie), occasionally humorous (Dogday Mornings). Always sick.
Dilated Peoples. Ev (The Weatherman LP -- check it out), Rakaa & Babu. Three times the illness. Worst Comes to Worst possibly my favorite rap tune of all time.
Az. Has enjoyed the shadow of Nas for all of his career, but is just as good as Nas, which is saying A LOT.
Vinnie Paz. Paz's Season of the Assassin was great but not JMT-like at all. See songs like Keep Movin' On, End of Days & Same Story for reference.
Jedi Mind Tricks. If you've never heard of them you've been missing out. Also check out Army of the Pharaohs.
Sadistik. A bit too emotional at times, but one of the most talented lyricists you'll ever hear, working with some of the sickest producers (Emancipator, Kid Called Computer) you'll ever hear. Forget Eminem.
Fresh Prince & Jazzy Jeff. Will Smith, who also gets a lot of crap for being popular. The stuff he dropped back in the Fresh Prince -days is unique, cheery and clean. Should get way more respect.
Adam Tensta. A Swedish electro-rapper, which might turn some people away, but definitely worth checking out. Has some great subjects and some very catchy beats. Not too radio friendly.
S.C.C Presents: Murder Squad Nationwide. Sounds like a bad old school gangsta group, which is what it is. WAY underrated, has some of the chillest old school tunes I've ever come across, like Who's Da Star and Ghetto Got Me Shadey.
Killah Priest. A Wu-Tang associate. Very underrated as well.
Cesar Comanche. The album Die In Your Lap is produced by 9th Wonder, need I say more?
Common (Common Sense formerly). part of the rap A, B, C.
And so on
There are a ton of great rappers out there, it's just that they aren't on MTV most of the time.