I'm going to agree with soopspoon (and a few others who've mentioned some Image titles) and say that some of them were well done and enjoyable.

WildC.A.T.S. (original miniseries)
Cyberforce
Wildstar
StormWatch
The Kindred
Spawn
Backlash
Maxx

But then, I'm a big fan of Jim Lee - and most of those came from his Image studio.

From DC - and I'm not a big DC fan - I really loved:
Kingdom Come
The Death of Superman
World Without a Superman
Reign of the Supermen/Return of Superman
Flash (Waid's run) / Impulse

I'm a much bigger fan of Marvel, and really did the bulk of my collecting from the mid-80s through the late 90s. I was mostly into the X-Men titles in that time and while there was plenty of dreck, there is also a lot of good:
Excalibur
Age of Apocalypse (all the X titles after this point took a nose-dive)
X-Men Fatal Attractions
X-cutioners Song (I liked the crossovers, so shoot me)
X-Tinction Agenda
Phlanax Covenant
Deadpool Circle Chase
while I'm not a big fan of the Spider-man Clone Saga, Spider-Man The Final Adventure was a good romp (and Revelations was a nice finale to the Clone Saga)
Star Jammers miniseries
Marvels

Dark Horse had a pretty good period at this point too, what with:
Star Wars: Dark Empire
Star Wars: Tales of the Jedi
Aliens (first and second series)
Aliens vs Predator (original miniseries)
Star Wars: Mara Jade By The Emperor's Hand

I didn't read any of their original series - there may be more good to be found beyond the movie tie-ins. Crossgen started in the very late 90s, so I guess it counts - and I really enjoyed Scion from them (Sojourn was pretty good too).