I was born in '94, so I'm a lot like you. I did catch several (mostly reruns) 90's cartoons when I was a kid, but didn't get to see a lot of the live action shows (and even some of the animated ones) until recently.
Well, 90's Nicktoons off the top of my head...
I enjoyed Doug. While I don't think I ever appreciated a full episode until rewatching the show recently, I did enjoy bits and pieces of whatever episodes I caught. I loved the colorful characters (and I don't just mean that in a literal sense), and actually thought Doug Funnie was a cool character (even though a lot of people considered him 'wimpy').
Rugrats has always been one of my favorite shows. I mainly love the 90's era of Rugrats. It was one of the first Nick shows I ever saw, and stuck with me from the beginning. I love the characters (the babies, adults, animals, and ficitional characters), and really enjoyed the adventure/imagniation concept (which is very similar to another show about babies that I think we're all familiar with). While as a kid I was usually annoyed by the babies lack of understanding of certain things going on in the world, now I love it. They're just babies. They're smart, yes, but they're still babies. Still, there were some episodes that I wasn't that fond of as a kid.
I really didn't care much for the 'solo Tommy' episodes (mainly the ones where he stays silent for most of the show). I found them to be rather dull, but there's always room for a second opinion. After all, I haven't seen a lot of these episodes in years. I also hated certain early episodes where Tommy would act sort of arrogant towards Chuckie. "Aw, come on Chuckie, don't be a baby". I don't know, I just found that to be an unlikable side of Tommy, but the character was still in development at the time.
There were also some rather sad episodes. We all remember the "Melville" episode, as well as the Mother's Day episode. Both tear jerkers for me. I also remember feeling kind of depressed whenever I watched the episode where Didi tries to get Tommy to stop drinking out of a bottle. Not sure why, though.
Dil's addition to the group definitely brought a change. But I really didn't mind most of the Dil episodes (especially since they were among the first ones I saw). In fact, I really didn't mind Dil as a kid. I thought he was funny/cute. Looking back on it now, Dil, while cute, could also be very disgusting at times.
I'd add more, but I should probably start a Rugrats thread instead. Unless there's already one on here?
I loved Hey Arnold! and I still do. Again, I'd add more, but this post is already getting rather long. I'll save it for future "Arnold" discussions.
Other shows like The Wild Thornberries, CatDog, and Rocket Power I thought were okay. And just okay. They weren't among my favorites.
The other 90's Nicktoons (with the acception of SpongeBob, which was just fantastic during its first season) I didn't really see until recently. Ren and Stimpy was interesting, I guess, but I haven't really seen enough of it to really get a feel for its style. Rocko's Modern Life was sort of weird, but funny. Angry Beavers was probably one of my favortes of these 'lost' Nicktoons.
As for the live action 90's shows, the only ones I ever really had a chance to get into were "All That" and "The Amanda Show". I'll admit that while I still find both shows to be good, parts of both shows just don't seem quite as funny when you get older.
I didn't get a chance to see Kenan and Kel until very recently (though I had seen Good Burger a few times). I really enjoyed the few episodes I got to see. So far, I've only seen one episode of Clarissa Explains it All. And I also remember catching episodes of "Salute Your Shorts" and "You Can't Do that on Television" (wasn't that a late 80s show?) during a little experiment that Nickelodeon's U-Pick Live (man, I miss that block!) did in the early 2000's. They let viewers vote from three different 'classic' Nick shows, and would air an ep. of the one that got the most votes.