Some of my non DC/Marvel favs:
Ultra by the Luna Brothers
Midnight Nation by JMS
The Crow by O'Barr
Maus by Spiegleman
DC/Marvel/Image etc:
Starman by Robinson
Lazarus bu Rucka
Gotham Central by Rucka & Brubake
Fables by Willingham
Nightly News by Hickman
Joe the Barbarian, WE3 by Morisson
Pride of Baghdad by Vaughn