Well seeing as I believe the 1990's to be the greatest decade for comic books this is a really hard question just because there's so damn many I don't even know where to start. But I'll give it a shot:

Savage Dragon
The Maxx
Spawn
Alan Moore's WildCATS
Trencher
Uncanny X-Men
Pollina's X-Force
Marvel Knights
SPlatt Prophet
Astro City
Marvels
Age of Apocaylpse
Hellboy
Waid's Ka-Zar
Clark's Alpha Flight
X-Factor
Early Punisher
Incredible Hulk
Spider-Man until 92
The Hunt for Xavier
WildStar
Cyber Force
Shaman's Tears

And many many more