I've played a few fan-made ones (like Paper Mario Online) but never to some degree of getting hooked. I'd like to try one, but until I find something I actually like to play, not really. If Nintendo ever make Pokémon somehow go online, I'd be the first to play it for sure. If Mario got an MMO from Nintendo, you bet I'd spend hours in it. But the PC generic ones, like WoW and all, haven't interested me much at all.
Games like Flyff and Wow are WAYYYYYYY too generic for me, it's just clicking a monster and clicking a number, watching an animation and repeating to level up.
I played:
Dragon Nest, Vindictus <-- It's WoW but more Action-ish, you don't just click monsters to auto attack, you have to aim all the skills.
Tales Runner <-- Sadly, this cute racing game got shut down this year, because of a very greedy developer.
League of Legends, Heroes of Newerth, Defense of the Ancients <-- For those who love tactic games.
Elsword, Dragonica <-- 2.5D Games, they were nice but they get generic and repetitive fast.
DOMO, Eden Eternal <-- Social MMO's that took the basic concept of WoW, added class change, cute looking characters and made it much less Grind-ish. (DOMO got shut down, after 3 (?) years of running)
Smite <-- Combination of LOL, HON and DOTA and Dragon Nest and Vindictus.
S4 League <-- Someone convinced me to try this shooter, I liked it, but the lack of maps to my favourite mode made me quit it after a month of playing it.
Atlantica Online <-- WoW, with a turn based battle system.
Oh, and if you're looking for a pokemon like MMO, there's the Digimon ones, Digimon Masters and Digimon RPG.
They both kept me playing for some short time, I would recommend Digimon Masters, but it has a lot of grind.
But for a real Pokemon MMORPG, There's Pokemonium if you want to play it.