Gotdamn there's alot!
Trap Muzik, The Blueprint, Be, Late Registration, No Ceilings, Dedication, Dedication 2, Trap Or Die, We Got It 4 Cheap (Vol. 1 and 2 but ESPECIALLY Vol. 2), The Documentary, Urban Legend, Graduation, Deeper Than Rap, The Black Album, Stillmatic...
This just off top, there was alot of good music and the 2000s is underrated! Even outside of good albums, I remember 2004 and 2005 being outstanding years for great music....
I'll think some more of this but the above list is albums automatically in my 2000s Vault, no questions asked!