Evil Genius, a world domination simulator, which I now see has already been mentioned, it's somewhat similar to Dungeon Keeper (which I can only recommend playing if you haven't done so yet.).
It's somewhat of a cross between RTS games and Themepark simulators.
You don't have any direct control over your minions, they'll automatically patrol and do jobs they're trained for, whether it's building (Which is what your basic minions do, all other minion training programs branch of from them.), patrolling, distracting pesky tourists or going out on missions away from your island to steal money or let's say steal the eifel tower with a shrink ray.
If you play it, I recommend reading the mission descriptions, they're hillarious. In fact, read every kind of description.
The world missions themselves are just a timer you wait for and every now and then you may see some of your minions get killed until they either succeed or fail.
All of the gameplay where you get to what people run around is on the island where you've got your evil lair.
You do get to directly control your henchmen (which are special minions, with special abilities) and your Evil Genius, which is... Well, you.
Minions near your evil genius will get their stats (such as loyalty and things that make sure they don't fall into your own traps) boosted, being near treasures also boost those effects.
Minions will desert if their loyalty gets too low and will try to escape your island, but your order your other minions to capture them and put them in a cell for a while, until they decide to be loyal again.
Also, minions really enjoy torturing and that will boost their stats, as well as draining the stats of the ones being tortured, depending on how your torture them.
Cutting them up with an industrial laser will kill them (Well, unless they're super agents, for who there is only one way to get rid of for each one), other tortures like putting them in a giant mixer will make make them dizzy or know them unconcious.
Another one similar to Dungeon Keeper is Impire, unfortunately, I've never been able to play it to the end because of some bug.
Yet another one like it: DUNGEONS (Yes, in all caps, possibly the Special steam edition.)
Overlord, well, you're an evil overlord, you're a villain, but there are other villains you have to defeat. They're pretty awesome. It does have a morality system, which pretty much goes from one end of evil to the other, depending on if you kill people or enslave them (litterally in Overlord 2).