Beast Wars would have to be the one, although, it hardly counts as a cartoon. There were so many great cartoons during the 90's.....I always look at the stuff now-days and think 'What the heck happened'
Rocko's Modern Life
Everything mentioned so far.
Rugrats.
Animaniacs, yo.
everything is wrapped in gray
i'm focusing on your image
can you hear me in the void?
I'd have to say Gundam Wing. It did come out on Toonami 1999 so it counts. X3