Who/what are the major intelligent undead monsters?

[Voadam]

I don't have any books with me, but I thought they could rebuke undead like an evil cleric or otherwise had some sort of undead control.

You are right. In Libris Mortis for 3.5 they can rebuke undead, but their main power is mind thrusting and having dominate and suggestion a few times a day. I was getting them confused with the 2e Ravenloft Living Brain which is very much mind control psionics and turns out is not even undead.

Nightshades always felt rather gamist to me, in that they mainly seem to exist to fill a slot for 'high CR undead' while not actually having the general backstory of 'once alive, but now not quite dead' we normally associate with undead.

They didn't used to have any background, just stats.

Undead Revisited from Paizo gives them a cool fleshed out extraplanar background. Similar for the Devourer.

 

[Rottle]

Death knights were fallen knights( mostly Paladins ) who failed to honor their order or vows in some big time way and are cursed into undeath. Often those knight who followed them and thus also failed either become death Knights themselves or skeletal warriors. Either way these are the only undead most normally command, they don't in general go around making or recruiting other undead.

Mummy Kings/Lords could be interesting undead leaders.

A lich who was a cleric instead of a wizard might be a good choice espically if they serve a God of undead.

Of course there is Vecna in greyhawk but he's actually a demigod now....