[color="#9932CC"][font="Microsoft Sans Serif"]As a principle, I'm never wildly fond of lava/fire-based or ice-based areas. For fire/lava, it's just being too paranoid that I'm going to fall into flaming hot magma and automatically die, but for ice, they're usually nothing more than slipping around. Pokemon's [i]especially[/i] bad about this, as every gen from Johto onward has had an ice puzzle of some sort, usually consisting of sliding around or walking on ice that can only be stepped on once. It's annoying as heck.
Oh, and warp puzzles. I don't think there's a single person I've met that actually [i]likes[/i] those.
Anyway, as for specific games...
[b]Majora's Mask[/b] has the Great Bay area. Now the area itself is actually my favorite in the game, especially since swimming around with the Zora mask is something every gamer must do at least once, IMO. So you have to rescue Lulu's Zora eggs. First you go to the pirate's fortress, which isn't too bad, but a little bit annoying since you have to play Solid Snake and avoid capture [provided you didn't sequence break and get the Stone Mask]. Then you have to go to Pinnacle Rock to get the last few. You're lulled into a false sense of security, thinking that "Oh, maybe they'll go easy on me in the temple, since I've already done all this much!"
Ha ha [b][size="3"]WRONG.[/size][/b] What follows is one of the most banal and annoying dungeons I've ever played. It's not fun, it doesn't make you think, it's just...annoying.
[b]Paper Mario: The Thousand-Year Door[/b] has chapter 2, The Great Boggly Tree, which is just taxing. Visually, the chapter is very nice, with black and white backgrounds with the characters in full color, but the second half of the level consists of you parading around a large group of creatures called the Punies, which are no taller than Mario's waist. First you start off with a small handful of them, then it [i]doubles[/i], and you're corralling around 100 of them. Oh, and if you happen to lose one? You have to go alllllll the way back to where it is and get it, because you have to have every last one to proceed. [Thankfully, this is made a bit easier with an item you can obtain that lets your current army stay in one place.] But overall, the chapter's just not a fun one.
But it's also rivaled by chapter 4, For Pigs the Bell Tolls, mainly because you backtrack. A LOT. You go back and forth between Twilight Town and the Creepy Steeple, which are a good several screens away from one another, and you have to do this at least...three or four times in the chapter. The chapter's length easily could have been whittled down and less irritating if they had some way to just warp you back and forth.
In the same series, [b]Super Paper Mario[/b] also has two of them. The first annoying one is, funnily enough, chapter 4 again, Outer Space. It's exactly what it says on the tin. The first and third parts of this chapter consist of you wandering around in space, where it is rather easy to get lost, and just kind of annoying. [Though the third subchapter is made rather entertaining. since it has you get chocolate from a cosmic convenience store]. THEN comes the final act, the Whoa Zone, which is basically this one giant maze in which you go through doors and defy gravity and UGH it's just annoying.
Then near the end of the game, we have chapter 7, The Underwhere. Later on, after getting yourself what is essentially the E-rated version of hell, you go into the E-rated version of heaven. During your time here, Princess Peach eats some sort of apple and falls asleep, and you have to go fetch the correct one to wake her up. Well, unless you have a guide in front of you to tell you which one you need to get, there's about four or five different apple trees you can visit. You can go around and collect one of each apple in one fell swoop, or you can wind up going back and forth between the trees until you find the correct one to wake her up. But the fact that each area looks almost [i]exactly the same[/i] doesn't help matters much, no matter which option you go for.
And...funnily enough, the first game didn't really have any chapters that I inherently disliked. I guess I'd have to pick the third chapter from the first game, if I had to choose one, cause it's not really that exciting.
[b]Super Mario Sunshine[/b] has the Noki Bay. It's a very pretty area, but the area itself just really isn't that fun, not compared to all the others. I guess it's 'cause it's kinda small? I dunno.
And going off James' post, the first [b]Sonic Adventure[/b] had Tails' levels, which, to me, were [i]very[/i] hard to control and just not that fun. And there's one stage in Sonic story mode, near the end, that was just so frustrating that it cost me a handful of lives before I finally finished it. I can't remember what the name of the stage was, though.
And [b]Adventure 2[/b] has Tails [again] and Eggman's stages, which were just...bad. They weren't fun, they were just boring and annoying. Bizarrely, though, I didn't mind Knuckles' and Rouge's stages for the most part.
Lastly, going back to [b]Pokemon[/b], pretty much every cavern. Seriously, Game Freak. Just stop. Nobody likes those. Nobody.[/font][/color]