Some interesting suggestions, but I was looking for something larger scale and more world breaking. Merly infinite wishes are not going to enable you to brush aside pantheons as a minor inconvenience to be slaughtered out of hand.
Also sacrificing your own believers for liquid pain and for blood is silly when there are plenty of people no-one will miss, or even better if you can take over your own country and get applauded for being tough on crime and doing something about the homelessness problem.
Believers make for the ultimate conspiracy fodder, perfectly loyal in case you need deniable ops or fanatic assassins. There is also no worry about infiltration as long as you stick to believers, though mind-reading and similar measures still risk discovery. And suggested mitigating process for these problems?
What i currently envision is an evil mega-corp with good publicity running the LE mendicant scheme of free healing for lots of reasons, one of which is undercutting the financial power of the temples, an other is to get ambrosia for crafting (we don't need no painkillers, we have nipple clamps... surgery is such a joy.).
Along side that run a conspiracy, using money and influence to get believers into positions like interior minister, or even king, since dealing with the paperwork yourself is far too much trouble.
If you had 10'000 years and 3 wishes a day as well as hundreds of expendable loyal minions what would you do? Especially if you knew that the gods will likely oppose your master plan, so you need to be able to kill a few dozen as an example so you don't need to worry about interference from them while dealing with more important matters.
Ooooh, I thought you meant something sane.
In which case, the gloves come off!
I submit transforming the thralls into a hivemind. They would still be under his control, and wouldn't count as thralls anymore.
Depending on how this is done, you could have a world-spanning hivemind, which would have an ECL of 9754, let's say (just a guess, anyway.). Grab the feat Reserves of Strength and smack those pitiful mortal armies with 4879 level draining missiles from a single casting of Magic Missile, or Shapechange into whatever you want, or trigger that old Arcane Supernova Bomb trick, which can cast (at the very least) infinite 1st and 2nd level spells with one action.
In other words, you rape the universe.
Alternatively, form the hivemind, and have a thrall that can use Psychic Reformation. You can turn your pet superorganism into whatever build you want, thanks to the class levels in [Whatever] that the thralls have.
Have you ever read about that build that created the Emerald Horde, which where practically invulnerable trolls? You can make them through a hivemind with epic levels.
Wait a second, epic levels? Epic Level Casting is all I'm going to say.
And he can still crowdsurf for style points.
Note: if hiveminds require below a certain intelligence to create, you can always use affinity field+something that creates intelligence damage.
