Plenty of choices to choose from here, but I'll go with an older one that not too many might remember.
In Breath of Fire, there is a dungeon called Mote's tower, or the dream tower, whatever. The reason this place sucks so badly is manyfold. It consists primarily of identical one space wide, many spaces long corridors that intersect each other in several places. The background being pretty much solid black.
At each of these intersections there is a fun tile that makes the black border zoom in so you can only see a few spaces around your character, and then it spins you round and round.
Now you are facing a new direction with up to 4 identical, non-distinguishable corridors to choose from. Before the internet, you would have fun wandering that surprisingly small area for an hour or 2 pretty much at random because there is literally no way to tell where you are going.
EDIT: This is what I am talking about http://www.youtube.com/watch?v=XLk7HUGQ0wE&feature=relmfu
Another fun one is the great desert in Breath of Fire 3. It brings the game to a grinding halt right at the end, for no reason other than probably one of the developers thought it would be cool to make you slog across the desert monotonously.
Also paying Tingle in Wind Waker to decipher maps, or whatever he did. That is just what everyone loves about Zelda games, grinding up thousands of rupees by sailing monotonously across mostly empty ocean in search of tiny bits of actual land with a chest or two. I could forgive it if it was an optional side quest, but its required to finish the game.
In Minish cap, you needed to collect every single figurine from the gatcha machine to get the final heart piece. Since this requires you to beat the game first, this effectively makes 4 pieces of heart and the final container completely superlative. You can only finish it AFTER you have finished the game. WTF do you NEED it for after you beat Vaati?
