Hip Hop left Dr. Dre, Eminem et al. behind alooooooooong time ago.
I share Cliffhanger's sentiments and would add a bit of..
CunninLynguists - A Piece of Strange
CunninLynguists - Oneirology
Kno (of CunninLynguists) - Death is Silent
RA The Rugged Man - Die Rugged Man, Die
Ill Bill - The Hour of Reprisal
Aesop Rock - Labor Days
C-Rayz Walz - Year of the Beast
Blueprint - 1988
KRS One & Buckshot - Survival Skills
Pete Rock - Soul Survivor II
Immortal Technique - Revolutionary Volume II
Army of the Pharoahs - The Torture Papers
Gangstarr - The Ownerz
Nas - Stillmatic
Cannibal Ox - The Cold Vein
Big L - The Big Picture
Murs & 9th Wonder - Murs 316: The 9th Edition
Little Brother - The Minstrel Show
Heltah Skeltah - DIRT
El P - Fantastic Damage
Cage - Hells Winter
Apathy - Eastern Philosophy
...to name a few...
And one could argue that the 2000s has very much caught up to the level of music that was put out in the 90s, however it has done so via the independent route as opposed to the mainstream. The 90s probably had the better production with the likes of Premo, Pete Rock, Large Professor, Dr. Dre, RZA etc running riot, however the new sampling laws restricts the likes of 9th Wonder, El-P, Kno and Stoupe, so only the best survive. Go and listen to some CunninLynguists and see how much Hip Hop has left Dr. Dre behind.