I got two:
Team Rocket Hideout, Celadon Game Corner. That spinning mania really grinds my gears. Plus, you move slowly too. What's worse, it's easy to get lost and you have to retake it over and over again.
And the pokemon mansion in Cinnabar too. I'm annoyed as heck when I'm stuck underground with the doors closed and out of repels. Same goes for other dungeons.