Stone Edge - For some reason, it just NEVER works when I want it to. In fact, the low accuracy of this move once cost me a position in a wifi tournament as Gyarados swept my team, all because this move had to miss and it was already gaining boosts.
Focus Blast - See stone edge.
Spore - an annoying ass move. I'm glad Gen 5 introduced more means of countering it, and I feel so proud to have an Espeon on my team to deal with that bastard Breloom.
Confuse Ray - that's what every ghost in Red and blue did, and it was just a pain in the ass.
Wrap (in Gen1) - Almost broken in this Gen. You couldn't move, and if your opponent is faster, they can keep doing it and you won't even get a chance to hit.