Oh boy, lots and lots of them. I didn't get Cartoon Network or Disney until around 1999, never watched Disney much to begin with, and then I abandoned pretty much all cartoons around 2003 for some odd reason.
Cartoon Network
Somehow, I never saw anything that they put out in the aughties until Chowder, which I watched through the recommendation of a friend and now consider a personal fave. About a year ago, another friend sent me a Life and Times of Juniper Lee episode on a whim, and I liked it. Among the other CN originals from the aughties, the only two that look enticing are Camp Lazlo and Sheep in the Big City.
Disney Channel
I dunno why, but I just never watched the channel much even when I finally got it! I picked up Gargoyles Season 1 on a whim and just LOVED it, so once I get more money I'm gonna pursue Season 2. Also, I checked out The Wuzzles and Gummi Bears online since both were before my time. I'm also thinking about going to Darkwing Duck, which somehow escaped my radar.
Nickelodeon
Somehow, as I mentioned in the Nick forum, I never caught a second of Ren & Stimpy because I knew it was grossout humor and everyone was annoying me by singing the "Happy happy joy joy" song. I should remedy that. Also, my first taste of Invader Zim was about 30 seconds of "Bolognius Maximus" which left me in a very long state of "WTF did I just watch?!" from which I never recovered until I finally gave the show a second chance in 2008.
Warner Bros. Silver Age
My cousins got me watching Tiny Toon Adventures and Animaniacs when I was about 5, and I abandoned it after maybe two episodes because I just didn't get that it was supposed to be a Looney Tunes homage; my Aspie mind thought it was a cheap knockoff. The only things I remembered were the theme and Montana Max. Since then, I picked up the first half of Season 1 (where the heck is the second set of discs hiding? I can't find it in any store!) also on a lark, and have found that the show was pretty darn good.
And as I've said before, I find Animaniacs to be 1 part funny to 37 parts annoying, so unless it's just the Pinky & the Brain segments (in which I found no annoying at all), forget it.
Also, like — probably pretty much everyone else here except Peter — I never caught Taz-Mania or Freakazoid! until they reran on CN in the early aughties. I found the former very pleasing and the latter, I have no recollection of except the lunacy of the theme song. Maybe Candle Jack erased the memories of
Other
Since I liked the first two Sonic cartoons, I thought I'd check out Sonic Underground. And I really, honestly like it. And it seems like I'm the only one.
Also, the original Biker Mice from Mars (hard to find that one anywhere!) and The Raccoons. Those latter episodes mix comedy and drama, and in a kids' cartoon... oh, and the music's awesome too. Lisa is the childhood furry crush I never had as a kid.