The only one I can think that ran for a little while was the cartoon with the people on mars it was called Red Rock or Red Planet or something like that. Also there was that Carmen Sandiego show.
I know some cartoons (both kids and adult) that were on Fox or have been on their since the 1990's
Kids:
Eek! The Cat
Batman: TAS (pre-WB eps)
Toonsylvania
Sam and Max: Freelance Police
Where In The World Is Carmen San Diego (I only remember two episodes of this show: a two-parter where Carmen finds her father and her father is upset that she became a criminal and this one episode where Carmen supposedly gets killed in an avalanche)
Animaniacs (pre-WB)
The Merrie Melodies Show Starring Bugs Bunny and His Friends
X-Men (none of that X-Men: Evolution crap; the real deal, even if the cartoon was toned down from the comic)
Spiderman
Silver Surfer (how long did this one last)
Taz Mania
BG & R originally aired on Fox in fall 1999. After four or five episodes, it was canned. It later had a full run on Fox Kids in 2001 and afterwards showed up on ABC Family.
I remember a show that was made into a game called Stupid Invaders for the Dreamcast and PC. I forget the name of the show, but it was about a bunch of aliens that lived in a house together on earth. Im almost 100% sure that this isn't the show though. Im going to say it's Xyber 9.