Oh come on, people! How in god's name am I the first one to mention the frickin' card game in FFVIII? That is THE biggest pain in the ass side-quest ever. Of all time. It doesn't help that it's obscenely tedious and takes an obscene amount of time, but it also actively requires maintenance while you're not even working on it or else the rules for the game just spiral out of control! You have to go around making sure the rules you want to play with are implemented across the globe and snuff out any upstart rules that pop up every now and then or else you end up with shit rules like direct-exchange, random pick, and playing blind.
Any side-quest in Dragon Age: Origins that requires you going into the Deep Roads. Why? Because fuck the Deep Roads.
Also regarding DA:O - and I know this isn't so much a side-quest as it is a side-track on part of a main quest - the dream sequence where the Sloth Demon puts you to sleep when you're trying to climb the mage tower. Having to go back and forth between those dream worlds, unlocking different forms and powers to use in other dream worlds, and the fact that a lot of the enemies in said dream worlds are pretty damn strong...it's all just one big hassle. It's a dungeon within a dungeon that's actually bigger than the dungeon it's contained within.
Hunting down Doomgaze in FF6. While the fight itself isn't too hard, it just takes forever flying around aimlessly to even encounter him and he always buggers off after you get a few hits in, meaning you have to chase him down again.
The Deep Dungeon in FFT. Filled with high-level monsters that can really mess your day up, but that's not even the worst bit. The worst bit is the fact that you can't see any of the terrain that you're walking on, and in order to progress to the next level of the dungeon you have to check every single frickin' square on the map in order to find the "exit". Hope you brought someone who knows how to put monsters to sleep. >.>
Any side-quest in Dragon Age: Origins that requires you going into the Deep Roads. Why? Because fuck the Deep Roads.
Also regarding DA:O - and I know this isn't so much a side-quest as it is a side-track on part of a main quest - the dream sequence where the Sloth Demon puts you to sleep when you're trying to climb the mage tower. Having to go back and forth between those dream worlds, unlocking different forms and powers to use in other dream worlds, and the fact that a lot of the enemies in said dream worlds are pretty damn strong...it's all just one big hassle. It's a dungeon within a dungeon that's actually bigger than the dungeon it's contained within.
Hunting down Doomgaze in FF6. While the fight itself isn't too hard, it just takes forever flying around aimlessly to even encounter him and he always buggers off after you get a few hits in, meaning you have to chase him down again.
The Deep Dungeon in FFT. Filled with high-level monsters that can really mess your day up, but that's not even the worst bit. The worst bit is the fact that you can't see any of the terrain that you're walking on, and in order to progress to the next level of the dungeon you have to check every single frickin' square on the map in order to find the "exit". Hope you brought someone who knows how to put monsters to sleep. >.>