In Chrono Trigger (the best RPG I have ever played and the only one I bothered to beat), The Golem Sisters and Giga Gaia.
I am not a fan of Hazy Maze Cave in Super Mario 64. Also, the shadow racing comet levels as Luigi in Galaxy can go die in a black hole.
I loved Twilight Princess, but if that wasn't a dull way to start a game I don't know what is. It's just random village quests, and I'm not too fond of the wolf bug collecting either. It didn't really pick up until after the third dungeon (with a brief bit of awesome in the Goron Mines).
I never beat my other favorite RPG, Final Fantasy VI, because of the Fanatic's tower. Seriously, no physical attacks?
The only reason I was able to beat Mega Man 2 was that I got Item 2 and thus could skip those damn disappearing blocks in Heat Man's stage. And don't even try to beat Quick Man's stage without beating Flash Man first, you will not succeed.
The Labyrinth Zone in the first Sonic was hellish and boring as much as you'd expect it to be in a game focused on speed and where the protagonist's weakness is water. Also on the topic of Sonic, the barrel in Sonic 3 was the one thing that really sucked about an otherwise very awesome game. Oh, and in Sonic Adventure 2, most people complain about Security Hall; I didn't even get there because of Egg Quarter and that goddamn egg beetle.
The moving platform and torch room from Turtle Rock dungeon in Link to the Past. You know what I'm talking about.
The Ferris Wheel in Call of Duty 4. You and a cripple verses the Ukrainian army in an open field with only some amusement park things. Have fun. Also Mile High Club.
And probably anything else that could be considered a scrappy level [http://tvtropes.org/pmwiki/pmwiki.php/Main/ScrappyLevel].