Don't tell me you think What A Cartoon!, Dexter's Lab, the Powerpuff Girls and My Life as a Teenage Robot (or the original Flintstones series and select shorts from Oh Yeah Cartoons and Random Cartoons for that matter) are lousy. Or the independent stuff Frederator's doing online.
But, whatever. Among my favorites are WB, Disney, Spumco, Bakshi Productions (also known as Bakshi Animation or Bakshi-Hyde Ventures, TMS, Wang Film Productions, and Startoons. Frederator gets a nod simply for letting cartoonists break loose with shows like Oh Yeah Cartoons and the aforementioned internet productions. The latter Hanna-Barbera (from when Fred Seibert became head of it in 1992 to its dissolution around 1999-2001) and Cartoon Network Studios (even to this day) have also done some very cool, creator-driven stuff. Klasky-Csupo did some amazing stuff like the early Simpsons, Rugrats, Duckman, and Aaaahh! Real Monsters, and even their later stuff, although generally disliked among animation fans, is most part not that bad IMHO. Among my guilty pleasures are Dic (only Inspector Gadget, Real GhostBusters and the video game-based shows I like, although I've heard good things about the Mysterious Cities of Gold or whatever it's called), and Nelvana (I have a liking towards Care Bears, BeetleJuice, and Eek the Cat!, and I want to see Rock & Rule). If we can count companies that aren't around anymore, MGM's cartoon studio in the 1940s and 1950s did amazing stuff, same with the Fleischer Studio.
As for my least favorite company, Filmation is pretty much at the top. The only good things about He-Man is that some writings had writing that was at least above average (like the ones by Paul Dini), and the stock rotoscoped animation sometimes looked a little smooth. Most of the rest of their stuff justs doesn't interest me (though their takes on Droopy and Heckle & Jeckle are like the Plan 9 from Outer Space of cartoons). I also must say that about 90% of the stuff Hanna-Barbera did from roughly 1970 to 1992 was pretty much awful. There was some decent stuff from H-B in the 1980s (like the Jetsons revival, Yogi's Treasure Hunt, and A Pup Named Scooby-Doo), but by the early 1990s, everything responsible for anything good in the 80's had moved on to WB or Spumco or Disney. No wonder Fred Seibert was made the head of the company (I admit to not knowing the whole story behind his entrance, though), and boy, did he turn that company around. In general almost every American animated TV show from the '70s (and to a slightly lesser extent, the '80s) was embarrassingly poor, but I don't really blame any studios in particular. It had more to do with focus groups and executive meddling from the networks than anything else.