Mine have been the Dark Brotherhood's and the Theives guild. DB because of the different ways to go about each quest and the Thieves guild because the sheer epic scope of what they ask you to do.
Agreed about the DB. Although I felt like the game almost forced you to take the alternative route.
I've been thinking over what I'd want to see in TESV.
Damaged armor and weapons. TES games have this now, but I mean visually. Like if you've just been through a big fight your armor will be all scratched and dented, and your sword will be chipped and notched.
more npc animations, I think they should license the facial animation technology from Valve, and add more animations to npcs. Like if the npc is wearing heavy armor, they'll walk a different way than if they're wearing light armor or a robe.
cloth physics, it really would be awesome to see an npc walking down a road with his robes flowing behind him.
I think they should improve on the npc scheduling. So their scheduling might include travelling to another city or even questing.
I think they should experiment with the npcs actually having relationships with each other. For example, there might be an npc that hates another one's guts, but in oblivion if they talk to them with the random dialogue they'll act normal.
more dialogue options for you and the npc. I think you should have dialogue choices that would make the npc respond differently and could change the outcome or goal of a quest. For example, in the mages guild quests there's a quest to get this amulet called the seer's stone. When you get it, there's this guy from the mages guild that comes and confronts you because he wants it for himself and attacks you. I think there should have been a choice for you to give him the amulet if you wanted too. also, more random dialogue options for the Npcs. "Hello." "Hello." "I saw a mudcrab today." "Bye." "Bye." doesn't really work. This is one way I think the relationships would work well, they'll act differently depending on how they like the npc, their tone of voice would even be different.
I also think it would be cool if some of the married npcs had families.
I think each npc should be hand designed with their own unique personality, goals, and schedule. Also, no voice recycling. I think each npc should have their own unique voice. I hear too much voice recycling for my taste in oblivion.
No more weapon and armor leveling. I don't think it works like it should. Each npc should have armor based on their talents and amount of theoretical money. Npcs should level up, but I think it should be random.
Maybe to counterract this they could have level specific quests. When your level goes up, new quests open up that might have higher level loot or enemies.
Dismemberment and gore. Bethesda has always seemed to make "family friendly" games. Well I'd like to see an adult oriented ES game. Sort of like an ES GTA. It would add something imo. And gore. Depending on your stats and luck factor, with one hit you might be able to kill someone by decapitation or incapacitate them by some other form of dismemberment. but it wouldn't always happen. That should be able to happen to you too. So you might be fighting and your hand could get chopped off, so you might have to resort to magic to get out of the situation. And you would slowly lose health (pretty slowly). And after the fight you could either bind it up, or get out of there and go to a special kind of healer to get it restored.
I think every npc and you should age as well, and with age the npcs will change in their behavior.
Some ideas I have. Please bethesda think like me.