As everyone must know by now, clearing certain dungeons before doing the required quest for them can really mess up your game. Especially for The Companions and Thieves Guild. The Raident system is meant to stop this happening but it seems to be as bugged as everything else. So does anyone know or have a list of all those dungeons which are best avoided? It's too late to save alot of people's saves but we can still help others.

This is one everyone who doesn't know that. I've done stuff like did quests in the wrong order or cleared a dungeon and then got the quest w/o seeing any bugs. In at least one case, the same dungeon was used twice by the game for two different quests and both worked fine.

I've seen that either the dungeon gets repopulated in the time gap between clearing and the quest or not. In either case, the dungeon isn't seeded with the foozle until the quest is triggered. Just yesterday I returned to a cleared dungeon on a quest and found the foozle seeded where it couldn't have been seeded when I cleared the place.

for me they either respawn or i get a quest completed message.