Wobbuffet was considered uber because it could lock in Pokemon with Shadow Tag and get a guarenteed KO. As Smogon says:
At first glance, Wobbuffet appears to be a pathetic excuse for a Pokemon with awful stats, sans HP, and a movepool that's as shallow as can be. If one cares to look closer, however, Wobbuffet can be quite a threatening force. It possesses the ability to either kill any Pokemon whom it wishes with proper prediction and the combination of Encore and either Mirror Coat or Counter. It can also use Encore to make a support Pokemon complete setup fodder.
You can run Encore, Mirror Coat, Counter and Safeguard (or tickle, but lol tickle) to great success getting at least one KO on a support Pokemon, or better yet, a sweeper. Safeguard also protects you from those nasty third-degree burns or toxic poison.
Also, it is also easy to predict what they are going to use. If you see a Mewtwo, there is a low probabiltity it will run physical moves. If you see Groudon, you are probably going to use Counter over Mirror Coat.
It also is not in Ubers anymore due to Generation 5 bringing a nerf to Encore, lowering it to four turns, and bringing the Gothitelle family as a standard OU Shadow Tag user.
Source for quote.