OK, now that I have time to type a proper response....
- Beast Wars. I have to start with this one. Beast Wars is one of those freak accident shows that is far too good for its time - being an expensive CGI show used primarily to promote a line of toys meant an absurdly good core cast of well-developed characters with a surprisingly well-told storyline...that regularly killed off the cast because it was too expensive to keep them in the show. It's the only time I can think of where being the product of cynicism and product advertisement has been benficial to a series. As far as I'm concerned, this is THE Transformers series. I've watched the classic show, I've seen the Unicron trilogy (which in all fairness wasn't bad, especially Cybertron, where Starscream really came into his own) and I've seen some of the more recent series, and...nothing compares to it. Plus it has David Kaye as the voice of Megatron...yes.
- The X-Men and Spiderman 90s animated shows. They're still the only TV series that get Marvel right - they adapted some of the best comic material of the time pretty damn well, looked great for their time, and...come on, everyone knows the 90s X-Men theme song.
- Batman: The Animated Series was something I didn't get to watch as much as I would have liked, but still enjoyed a lot - the entire DC Animated Universe was of a comparable quality to the Marvel one running at the time, although it was significantly darker. This is also the only Batman adaptation to get the Joker right. It also led to Mask of the Phantasm, the greatest Batman movie of all time.
- I say this, but I am going to give a shout-out right now to Batman: The Brave and the Bold for giving us the Music Meister. It's over 10 years old, so it counts as nostalgic...and it's the voice of Neil Patrick Harris; you can't argue with that kind of quality!
- Freakazoid was, and is, hilarious. Like The Mask, only...much better. As much as I enjoyed the film of The Mask, the TV series sucked. Same with Ace Ventura. You just...can't replace Jim Carrey.
- Of all the Sonic TV series - of which I have seen all of them - Sonic Underground is probably my favourite because of the songs. It was SO BAD yet at the same time getting a song basically every episode was so good. I was kinda annoyed it never really resolved itself though.
- I grew up watching the Smurfs...and the classical piece that plays whenever they're in trouble STILL eludes me!
- Street Sharks and Biker Mice from Mars were my original badass cartoons that I had toys of...god, the reboot of the latter, what did they do...
- Gargoyles deserves its reputation as one of the better cartoons of its time.
- Wacky Races and Stop the Pige--I mean, Dastardly and Muttley and their Flying Machines. These were my before school cartoons of choice, alongside Thundercats, Secret Squirrel, and occasionally the original Teenage Mutant Ninja (Hero) Turtles.
- Tom & Jerry and, to a lesser extent, Tom & Jerry Kids. Tom and Jerry are responsible for my appreciation of classical music; I spent YEARS tracking down some of the pieces I heard in episodes, and even now when I hear a piece on the radio I can playback the episode that uses it in my head. I've probably seen every episode of the classic series. "Snowbody Loves Me" and "The Cat Concerto" are my favourite episodes.
- Looney Tunes, up to around 2000. I've seen pretty much everything up to and including Sylvester and Tweety Mysteries, which I loved...well, I might not have seen some of the REALLY old stuff, but this was a staple of my early childhood. Taz-Mania is an interesting one that I hated as a child but absolutely love as an adult because all of the adult humour that went completely over my head back then. I kinda lost interest when they went with Baby Looney Tunes - sorry, but the only baby cartoon I'm prepared to watch is Rugrats - but everything prior to that I enjoyed. Rabbit of Seville is a great episode.
- Pinky and the Brain is still gold, it's the perfect balance of slapstick comedy and very dry adult humour...and Gilbert and Sullivan song parodies. I was never particularly fond of Animaniacs (although I DO know the Nations of the World song) but I loved Pinky and the Brain.
- Darkwing Duck was awesome. No more need be said.
- Super Robot Monkey Team Hyperforce Go! is the closest I've seen to animated Power Rangers...one of the better Disney seasons, like Jungle Fury or Dino Thunder, at the very least. Maybe not RPM level, but still great.
- The first two seasons of Jackie Chan Adventures were great. It was the first time I watched a show where the Chinese Zodiac were used in anything and they had a magazine with metal talisman keychains on sale at the same time it aired...I never got them ;-;
- Mummies Alive! was a pretty cool cartoon I watched in the early 2000s about revitalised Egyptian Mummies that had transformation sequences. This benefited from a very small cast and a pretty unique premise.
- The first two seasons of Winx Club were...surprisingly good, actually. A good villain makes a good TV show, and Lord Darkar definitely had presence in the second season. I also appreciated that every girl was given some form of character development even though it was initially very Bloom-centric, and their ENTIRE lives didn't revolve around their boyfriends. A great deal of their lives, but not all of it.
- The Watership Down TV series was great, although not quite as traumatising as the 70s movie. I'm not sure if that's a good thing or not...General Woundwort from the movie is the most terrifying thing you can see when you're an innocent five year old who adores bunnies. The third season wasn't particularly great either, after they swapped out the majority of the voice cast.
- Totally Spies was amazing up until around season 3. I was kinda disappointed that Mandy becoming a spy was only a one-off episode though, and that Britney wasn't in it very much, because she was my favourite.
- Teenage Mutant Ninja Turtles, up to that AWFUL Fast Forward season, was a great reboot. The 2002 Masters of the Universe reboot was fantastic as well and I am still very sore that there was never a second season...it was another show that was ridiculously violent considering the target audience and the time it aired on TV.
- Arthur. Everyone's watched the earlier seasons of Arthur, right? The musical episode was so good.
- I'm gonna give a small shout-out to Storm Hawks if only because of Ravess. Villains who insist on their theme song being played whilst they go into battle are the best kind of villains. It was a terrible show, but that one thing made me come back to it. xD
- When I was REALLY young - like, 7 or 8; before Pokemon - one of my favourite series was Noah's Island. It was made by the creators of Animals of Farthing Wood, which I also really enjoyed, although honestly I preferred the books of that. Really strong characterisation (Sasha needs to go away though) and a nice theme tune, too. My brother still watches it on his iPad sometimes. xD
- Can I show my age and say that I remember watching the 90s Rupert TV series? That was actually a really good show...like Moomins, only not nightmare fuel.
...I think that's everything. For now.