At the moment some of my favorites from when I was younger are those that I mentioned.  I used to love Transformers, but I can't remember watching it much.  Teenage Mutant Ninja Turtles, obviously.  Pirates of Dark Water was a good one, imo.  He-Man was another major one, but I haven't watched it in decades.  As mentioned earlier I want to revisit the Ghostbusters series.  I watched the Back to the Future cartoons, but I don't recall them having quite the impact of the movies or other cartoons I listed.  I have a hard time remembering a lot of the 80s and 90s cartoons.  I have watched a couple compilations of opening theme songs on YouTube.
*Consulting a list*  Scooby Doo is ok in most of it's iterations.  It was playing while I was working on something the other day and there was this goth girl band playing.  I later found out they are in a few episodes and movies, so I might try to track those down.  While on the topic of music, Alvin and the Chipmunks from that era was something I watched often.  I guess I like cat cartoons because I watched both Garfield and Heathcliff.  Beetlejuice (maybe I like cartoon goth chicks).  Fat Albert.  Fraggle Rock (both versions) and Muppet Babies.  I am pretty sure I liked G.I. Joe, but I don't remember watching it much.  Mr. T. My Little Pony, Care Bears, Rainbow Brite.  I will finish up the 80s and add some 90s cartoons later.
Some Disney stuff was good: Duck Tales (and the games!), Tale Spin.  Some of the others had some good story arcs or episodes, but I wasn't super into like Aladdin (the series) and Rescue Rangers.  I think my absolute favorite Disney cartoon series is Gargoyles.  Oh, almost forgot Gummi Bears, another of the greats.  Maybe others.
Some modern youth oriented ones I like are Regular Show, The Amazing World of Gumball and Steven Universe.  Tron: Uprising was good, and I feel they should have made more episodes...oops, I seem to have wandered back into Disney.