1. I will never require any teenager within the town limits of my empire to choose a single faction to devote themselves to for the rest of their natural existence. Furthermore, since the risks always have a nasty tendency to outweigh the rewards (and it rarely ends well), there will not be any such factions in the first place. (Of course, there are other ways to find out what drives them.)
2. I will always make sure my Legions of Terror have plentiful supplies of winter uniforms.
2A. Following up on that, I will never invade a country where said uniforms would be necessary to survive in the winter.
3. Unless it is an absolute last resort, I will not hide out in my grandmother's basement. Eventually I'll have to go to the bathroom, and chances are the old bint will find out and rat me out to The Hero's pals.
4. If I have a project to create a defense system that makes defending my invaded territory/colony easier, I will treat the workers well and give them their well-deserved occasional vacations, food and wages. This may cost more, but this will save me the even larger cost of being labeled as an evil tyrant and given and Historical Villain Upgrade in the future.
5. My mooks will learn how to fight in large groups to further reduce the chance of being affected by the Conservation of Ninjutsu.
6. My Legions of Terror will never wear name tags. What was it you said about tattoos again?
7. I will imprison any Fanboys and Fangirls because they often cause problems.
8. If I ever get into a debate with the hero, I will assume that the hero is a skilled debater and I should treat him as such. Avoid using fallacious arguments and do not be afraid to point out and explain the fallacy (especially Ad hominem and Poisoning the well fallacies).
9. It might not even be a good idea to usurp the throne of my noble half-brother (see original Rule #3). If one of my trusted advisers or lieutenants suddenly informs me it’s a mad scheme… they can probably find far better uses for an iron mask. Besides, I might actually need his help later on.
10. When punishing my minions, I will not kill them (with the expectation of a heel-face turns) or spam the agony beam as they tend to lower morale and cause Mistreatment-Induced Betrayals.
11. Continuing Rule #2 if the heroes have a Team Pet that is small enough to crawl through the ventilation ducts I will add surveillance cameras in the ducts.
12. Going Go-Karting with The Hero and other assorted cast is always a good idea. Morale is boosted if the Evil Overlord is seen doing something actually human and having fun for once.
12A. Unless it's more than just Go-Karting...
13. The plexiglass to be used for the visors on my soldiers’ helmets (see Rule #1) will be anti-scratch and anti-glare. Something called Crizal, perhaps?
14. I will keep a record of all previous structural renovations to all my buildings. If I acquire a new one and only if I plan on keeping it, I will have professionals and 5 year old kids scour every nick and crevice, just in case there's some secret passage or a basement that wasn't in the original plans.
15. I will regularly train with an Old Master (or two) and make sure my Legions of Terror regularly train with a variety of Old Masters themselves. After all, how do you think they became Old Masters?
16. I will not pass off my opponents as all Card Carrying Villains or otherwise Always Chaotic Evil. Instead, I will paint them as well-meaning but misguided. That's easier for the public to swallow.
16A. Heck, I will do this even if I am Obliviously Evil or not evil at all.
17. I will simply push the hero into the shark pool instead of hanging him above it.
18. Dating is a risky prospect. The song goes: “A pretty face can hide an evil mind.”
18A. Of course, there’s nothing at all wrong with The Hero dating.
19. No matter how remote the possibility may be, I will always keep in mind the possibility of a god, gods or god-like entity existing and assisting the hero, a la The Odyssey.
20. If the Hero is beginning a transformation sequence, I will either shoot the Hero as s/he is undergoing it or increase my weapon's power as it occurs, rather than merely standing and gawking at it.
20A. Alternatively, I would withdraw while he's distracted with said sequence. Eventually, he'll turn back into his normal form, convinced that the battle has ended. At which time I shall have him shot dead from sniper range while his transformation powers are on cooldown.
21. If I threaten to destroy the beautiful princess's hometown/city/planet if she does not give up critical information, and this pressure results in her giving up said information, I will not destroy the hometown/city/planet anyway. I Gave My Word. Of course, this automatically invalidates if she gave me false info.
22. I will not do Sex Slavery ever. Power Is Sexy; there are probably millions of women in my kingdom who will happily jump into bed with me.
23. I WILL leverage any relationships the brooding Anti-Hero on the verge of a Face-Heel Turn is in to my advantage, especially if they are part of a monastic order that forbids romance/marriage.
24. My base of operations will be a nondescript average-sized building with no visual displays of any sort. Rest assured, a legitimate business where you rent out your quarters will not hesitate to rat you out if The Hero and his pals come knocking.
25. I will train My Dragon to snap me out of atemper tantrum.
26. If through some method, I have obtained my second in command or other allies by manufacturing a tragedy that caused them to join me, I will never ever reveal to them that I was the one behind it, no matter how loyal I think they now are (See rule #189). That is just a free Heel-Face Turn waiting to happen
27. I will never ever tell destructive weapons to converge on my position. This is particularly true if a) the units destroy based on certain criteria no matter what, or b) the units are just forces of destruction that destroy everything no matter what. Even if the hero is at my location, I will not say this: anything can happen in the time between my summons, and the time the units arrive. Circumstances may occur such that I, or something in/on/around me that I don't know about/can't immediately remove/can't reach, wind up fitting the profile of my weapons' target, and if I state my position, I've guaranteed that my own weapons will chase me down wherever I go. Instead I will summon them to a fixed position that I know I can flee in an emergency, that isn't dependent on where I am.
28. My planetary-destruction weapon can be tested just as well by firing it at a desolated, uninhabited planet.
29. If La Résistance is on the verge of overthrowing me, I will not break out the nukes/planetary bombardment/Death Stars/whathaveyou. Chances are, if they've gotten that far, the populace probably supports them and breaking out the aforementioned weapons would only increase that support. I will instead try to negotiate a deal whereby I am allowed to live in relatively affluent exile, or just flee the kingdom.
30. I will NEVER personally supervise any high-profile construction, especially if it's for military purposes. I prefer NOT to give La Résistance excellent chances to kill me, thanks.
31. I will not forbid any school, camp, campaign, or community organization under my jurisdiction to ever have a public show. Good PR is not always overrated.
32. Under zero circumstances will I hotwire – or encourage anyone else to hotwire – any musical instrument for the express purpose of disposing of The Hero. Neither Murphy's Law nor Finagle's Law play favorites.
33. I will ALWAYS have no less than 3 Outside Context Villains to get the call on speed dial whenever necessary.
34. If the hero has a very strong compulsion to never take a life, then I will take full advantage of it. Though of course, you never know when a semi-pacifist hero will snap and make an exception for me.
35. Considering how it usually turns out, I will not waste any time when I encounter the hero. I will immediately try to kill him on sight without delay; I will not take him prisoner, nor have any conversation, nor will I use any slow means of killing him.
36. If I ever decide that retreat is a good option, I will attempt to salvage as many high ranking officials and appropriate mook squadrons with me. This ensures that I will not look like a jerkass to my minions and that I might legitimately care about their well being. Boosts morale, even while we're all running away.
37. Related to Rule 44: Before hiring any Bounty Hunters, I will make absolutely sure that no one within in my own ranks has the skills to carry out the same task. Hired Guns run the risk of being paid to turn against me if The Hero can offer them more money than I can.
38. An accountant and / or purser is never a bad idea.