^

lots, from KH2's 100 Acre Woods minigames to Warcraft 3 optional quests in any levels there

The hunts in Final Fantasy XII were fun and challenging to do. There's also the re-matches with the Glohm versions of the bosses in Mario & Luigi: Brothership that were really challenging (got my first game over back then) to me. 

There's this one small quest in Skyrim where there's a few Redguard mercenaries from Hammerfell looking for this specific woman in Whiterun because she's wanted for treason. However if you go to her, she denies that she did anything wrong. It's up to you to decide who is telling the truth with the limited information you have. You can change your mind at any time during the course of the quest, and there's no dramatic reveal or plot twist the 100% tells you if you're right or not. You just have to trust what you know of the world, and your reasoning. As someone who had never played any of the elderscrolls games before Skyrim, it was nerve-wracking in the best way.

The skateboarding minigames in Spyro year of the dragon were always fun (except for the skateboard races)