Opinions will of course vary, but among my favorite third party settings include the Iron Kingdoms, Dark Legacy, Midnight, Freeport, and the semi-official Rokugan. Late in the 3.5 era we get Golarion, which was later updated to Pathfinder.
Eberron was from that same era, and Dragonstar, and Urban Arcana, and Sovereign Stone (which, granted, is more interesting to me because of its alternate classes than for the setting itself) and I've got a long list of settings that I quite like. If you go just a little further afield and include stuff like Lizard's Mars or Iron Lords of Jupiter, then you've got even more options.
Keep in mind, I'm a dyed in the wool, ever-lovin', dedicated homebrewer. I don't really play in
anyone else's setting very much. Heck, I even modify Star Wars significantly when I run it, so I can make it do what I want it to.
That said, almost all of those settings were ones that considered good enough to buy, keep, and borrow from liberally.