For me it depends on the genre I feel like watching. But Record of Lodoss War always will be a hit because of the story, the art, and the whole medieval feel. Key: The Metal Idol is an often overlooked story set in the near future that makes for a suprizingly good suspense series. Cowboy Bebop and Outlaw Star go back and forth for wild west style action. Though Trigun isn't bad. Noir barely gets edged out in the "realistic style gunplay" arena by Gunsmith Cats. That show is just too good. Ghost in the Shell: Stand Alone Complex definately takes the futuristic action crown, good story, well developed characters, and excellent art. I haven't seen a mecha anime that I really would place as one of my favorites. I've seen all of Eva and was majorly not impressed. I've also seen a bit of Macross, Gundam, and was a fan of Robotech and Voltron when I was a kid. For the silly/cute series, I have to place Chobits.
In the end though, Record of Lodoss War gets the crown, with Key being a runner up.