Well, in the end, each decade has its gems, and each decade has its crap. The crap tends to outweigh the gems, but that is true of everything.
The 80's had gems in "The Real Ghostbusters" and "DuckTales." If I had to pick the two top quality shows of that decade, those would be the ones. Sure, I enjoyed others, but I find them hard to watch again without cringing.
The 90's was different, and I credit Bruce Timm and Alan Burnett's "Batman the Animated Series" with cartoons really growing up. It gave other production companies the courage to attempt to equal or better it (whether they succeeded, your mileage may vary). But we got "Gargoyles" (yes, I had to mention it, you know me), and "Beast Wars" later on. Timm and Burnett brought us "Superman TAS," and then "Batman Beyond" as that decade came to a close. I've also got to mention the unsung and mostly forgotten "ExoSquad."
The 00's are fresher in my mind, for obvious reasons. I think we had a lot of gems. My personal favorites being "Avatar: The Last Airbender," "The Spectacular Spider-Man," "The Venture Bros," parts of "Teenage Mutant Ninja Turtles," and "Megas XLR."
There's been crap in all of these decades also, and we all have our personal lists, but that's beside the point.
And, I apologize for the tangeant, but the DCAU is really Bruce Timm and Alan Burnett's. Alan Burnett was Paul Dini's boss, and Bruce Timm's partner on these shows. He executive produced the entire DCAU, and I have no idea why Dini (who did spectacular work on the DCAU and was one of the chief architects, don't get me wrong) gets Burnett's credit.