Gen 1: Misty. That Starmie was horrific. I hated the thing; not only was it really fast, it hit so hard for so early in the game.
Gen 2: Whitney. Ugh, everyone knows why. That Miltank is the biggest ass in the pokemon world. Doesn't help in HG/SS it holds a Lum Berry, either >.>
Gen 3: I thought Norman was pretty hard, even with Truant those Slaking were still always ~4/5 levels higher, and had decent bulk and could hit hard. And once you had them beat Vigoroth would outspeed everything and just kill all your already weakened pokes. Tate and Liza were also pretty annoying to face, especially in Emerald with the Claydol and Xatu. But I think I'm going to go with Norman.
Gen 4: Umm, none were really that hard, imo. I suppose Volkner was slighty harder than the rest, so I'll go with him and his tricky Electivire.
Gen 5: Probably the first gym (whichever one you get). The type disadvantage is unfair, especially when I don't want to be forced to catch and train a silly Patrat or Lillipup to beat them or use the Dreamyard monkey, none of which I like. I finally managed to beat Cilan with just an Oshawott after many hours of trying though. Work Up + Vine Whip was murder.
Lenora supposedly causes trouble for a lot of people, but her Watchog never caused me any trouble whatsoever, so I can't vote for her. xP