Stunfisk. The first time I saw him on Black, my reaction was literally WHAT THE HECK IS THAT??? I didn't even know if it was supposed to be a water Pokemon, a ground Pokemon, an electric one or what at first. All I knew was that it was the ugliest freaking Pokemon I've ever seen.
And Musharna. It kind of resembles a... fetus... which kind of tripped me out the first time I saw it. Especially since it evolves from Munna. I think they honestly should have made the evolution the other way around. Either way, it's a weird looking Pokemon.
Nosepass and Probopass, though, are probably the weirdest in my opinion. Rocks with big, red noses... and one has a mustache, too... interesting...
ETA: And I almost forgot about Mawile. When I first saw that thing when I was younger... I didn't know which part of its body was the front and which was the back! That whole mouth thing on its head is just weird!