I have to say that cartoons in the 90s were some of the best out there, I miss a lot of them considering the horrible quality cartoons of today. Some of my favorites were Ed, Edd n' Eddy (those guys are so dumb bit really funny!), spongebob, the Simpsons and Rugrats. I am always comparing the good cartoons of the 90s with the ones of today and all I can say is...what a difference....we go from shows like this to stuff like adventure time and uncle grandpa and stuff like that. A good portion of the cartoons of today use vulgar and crude humor to come off as funny...it's just not the same... 

Ren and stimpy undisputed number 1, invader zim is up there too.   

From the 90's, I really liked ed edd and eddy, that was a really weird and hilarious show.

Dude the 90's had some of the best cartoons of all time! It seemed like the silver age of cartoons (the old tom and jerry other cartoons of that nature being the golden age). Some of my favorite cartoons from that time are Tail Spin, Duck Tails, Darkwing Duck (is that what its called?), Pokemon, Yu-Gi-Oh, and so many more awesome shows.

GenesisJunkie :

Duck tales, Tail spin, Darkwing duck...

Oh the Saturday mornings of my childhood could have not been better spend!

90's Simpson are still pretty funny considering I haven't seen most of them.

I never watched lots of 90's shows but i have probably watched that one the most. They look way different then and now

I really liked Ren and stimpy dun be making fun of it. I also loved catdog, ed, edd and eddy, and hey Arnold.

My favorite 90's cartoon is Duck Tales. It was one of the best things that Disney has ever made.

Technically, South Park came from the 1990s.

However, as far as kids' cartoons go, Rocko's Modern Life is clearly my favorite 90s show in my opinion. Sure, it's not appropriate for school, but it's fantastic regardless. It is like Spongebob on steroids (no, not LSD, steroids).

Well, I was born in 1999, the final year of the 90s, but I did see re-runs of a lot of 90s cartoons. The most memorable are:
-Rugrats
-Hey Arnold!
-Powerpuff Girls
-Dexters Lab
-Ed, Edd and Eddy.

farmboy8 : Rocko's Modern Life was a ridiculously solid and well-written kids' sitcom with a lot of clever satire mixed with kid humor, and nearly every episode was actually pure genius in its own special way. I don't really mind the adult humor, as it is actually kind of an adult/teen show in general when you look at the concept. Also, it is literally Spongebob's father, and had higher episode quality than Spongebob ever did for the most part. Show some respect, your overprotectiveness.

My favorite 90's cartoon is the animatiacs because it also had this show called pinkie and the brain

It is insane trying to decide, because I watched and adored so many of them!
I think at the time it was a tie between Dexter's lab, Pokemon, and the Powerpuff Girls.
Looking back... it's probably just Dexter's Lab. I still enjoy the show (Though the Animaniacs and Digimon are still a ton of fun, too)

I guess my favorite cartoon for the 90s would be thunder cats. it came on right after school. it was also a plus that Mumra scared my little sister.

My favorite 90's cartoon will have to be Daria. It was made and shown in the late 90's and early 00's and her sarcastic undertone was humorous to me at that young age. As I got older and watched it again, I could truly appreciate all of her insults and everything that show had to teach about society, popularity and friendship.

Hands down my favourite cartoon of the 90's was X-Men: The Animated Series. I still love it and watch it on DVD every now and again. 

My favorite 90's cartoon was Doug. It was back when Nickelodeon was a good channel. It's about an 11-year-old kid and his intelligent dog, and basically Doug has to deal with everyday life. And not to mention the pilot episode has a Super Nintendo reference. Yeap, Doug gets addicted to the "Super Pretendo"

My top favorite was Rugrats hands down. I grew up watching and and my Dad and I would watch it together all of the time when I was younger. Those were the simple days. When I had like a 10 inch color TV. I also liked Amaniacs.

The Decade of the 90's had a lot of very good cartoons, be it those that had their debut during the decade or those that were still running or re-running from the 80's. I mean here is a list of shows that I watched:

Chip&Dale Rescue Rangers
DuckTales
Darkwing Duck
Tailspin
Gargoyles
TMNT
Spiderman Animated Series
Batman Animated Series
Superman Animated Series
X-Men Animated Series(anyone noticing a pattern here?)
Animaniacs
Pinky&The Brain
Rugrats
Rocko's Modern Life
Doug
Thundercats
GI Joe
Transformers
Tiny Toon Adventures
Dexter's Lab
PowerPuff Girls
Johnny Bravo
Cow and Chicken
Reboot <- very underrated and an early CGI show

and I could go on... LOL
 
Even a few shows from the early 2000's deserve to be on that list like Code Lyoko and Teen Titans. If I had to pick one show from that list, I would probably have to go with Pinky and the Brain. "The same thing we do every night Pinky. Try to take over the world!"