I always have autonomy on, even for my main Sim and even if I only have one Sim. I like it when the game tells a story just based on the autonomous actions. But I do have some mods that stop certain auto-actions such as drinking from the sink or mourning at an urn/gravestone.
Then again, I control my Sims in certain situations. But when I do, it's either for repairing/upgrading something, for filling their needs or for storytelling purposes. For example, I can't imagine anyone but an insane Sim to not shout at the Grim Reaper and insult him after he took away a relative or other beloved person. An insane Sim on the other hand would chat quite friendly with him, and a romantic one (that is Very Flirty) would instead try to seduce death (especially with the Serial Romantic aspiration).
But that's just me trying to keep the game a little bit realistic (this doesn't mean that I don't play with aliens though, it's more about the unrealistic emotional reactions that bother me).
And the other case where I take full control is when they have a whim. I always make them sticky so they don't go away (unless it's a whim to greet someone who already left the lot) and then try my best to satisfy that wish.
