You know, I've been meaning to bring this up as well. The 90s were sort of this 'dark age' for comic books, and a lot of people are still pretty jaded by the whole thing. But dammit, I came up in the dark age and I have a lot of fond memories about it.
Now I'm not gonna get all sappy and nostalgic about some shit just because I was 12 when I read it. There's a whole lot of crap that came out in this decade. But I'm gonna rack my brain here and try to think of some good that came out of the 90's. Here's a mental rough draft of possible contendors:
Independent/Alternative comics - Not just the quality of the titles themselves, but the market for them as well. Let me do some research and see if this holds water. Generally I associate the 60s and 80s with independent booms, but you did have things like Vertigo & Image which sort of brought about this mainstream-meets-the-underground brand of comic book.
Diversity - There was a period here that really focused on these superstar comic artists, and for all the damage it probably did there was still some silver lining. I think this is where you really saw a diversity of art styles develop.
Coloring - All right, I kinda have a tough time admitting to this, since there's a lot of over-photoshopping going on even today, but come on. In the right instance, digital coloring looks pretty kickass. Those gradients and shading techniques in Spawn were mind blowing for their time. Yeah, I said it.