Maybe the topic should have been "best MMO you've ever played that's not WoW" since most people are going to say WoW, lol.
I don't really have a "best" anymore. I'm just going to go with stuff I liked in the following mmos:
1. WoW before Cataclysm. Wrath wrapped up the last of WC III storylines which I really liked. Also loved Burning Crusades' latter raids for the same reason. After Arthas' death, the bottom dropped out of me wanting to see "what happens next" in the game.
2. Lotro during Moria and Mirkwood expansions. Thought Moria was impressive in terms of open world dungeon design (not meaning instance), world builders might have done too good a job judging by peoples' tears about it being too dark and well...full of orcs. Think LotRO's Moria as whole buried WoW's BRD tbh. I also liked the Dol Guldur raid in Mirkwood.
3. The Secret World. I still love this game, warts and all. And the warts keep it from being considered "best" sadly. The devs are still putting out content I'm interested in playing and I think they do story telling better than SWTOR. Well, at times it feels more story "texture" than narrative in their quests, but I like that they're asking the player to figure things out for themselves instead of spelling it out for them. And whoever thought to just have players cash in quests with a cellphone is a god amongst devs. I do wish they opted to teach new players how to solve the time to kill puzzle for themselves (i.e. small early tutorials on how to make better use of the ability wheel) instead of taking a nerfhammer to all the mobs in the overland pve. The only redeeming thing about TSW combat itself was learning how to leverage the wheel to your advantage.