Secrets of Loc Muinne. I thoroughly enjoyed it, makes a refreshing change from the "go there, kill that" kind of quest. For me, it's one of the more memorable quests in the game.
Ya I feel like the ones where they are multi-staged (which usually means longer and more complex quests), and like you mentioned in an earlier post - ones that have semi main characters added into them are usually the more memorable and meaningful quests.