I will assume the hero is genre savvy, even if he has been shown to be an idiot hero as that could just be a ruse to make me feel too secure in my victory.
If my opponent really is an idiot hero, then they will have an intelligent but cold ally that the hero will rarely listen to. I will kill this person before the hero can teach them about instinct and friendship, since after they learn about that, they will become a realistic threat to my plans.
Before my rise to glory, I will kill all of my past mentors/teachers and replace them in their schools with substitutes and explain that said mentor/teacher went abroad to study. I will also make sure to silence all witnesses.
I will leave various communicators laying in the ground where ever I go that ring any theme tunes associated with me when they sense the vibrations of people's footsteps. If answered, it will explode.
If behind an unbreakable force field with my enemy trying to get in, I will also pay attention to all other degrees of vision. Chances are my unbreakable force field is, on the contrary, breakable, and it just so happens something ready to break it is nearby.
Should time travel become available, I shall send a team to my parents when I am an infant, and proclaim a fake prophecy that I am a chosen one. They will also launch a propaganda campaign about my false prophecy, scoring good publicity and making my path to power easier.
Another time travel team will be sent to the pasts of any heroes and other enemies, where they will use any means possible to ensure that they won't grow up to become a threat to me. Whether this involves killing them, or covertly changing their lives will depend on what's more convenient.
I will maintain a healthy sense of humor about all aspects of my life. Then, if the hero attempts to goad me into making a rash mistake by mentioning something that might be a sore topic for me, I will simply laugh, say "You got me there!" and shoot him. Between the eyes. Twice.
My lieutenants will be expected to have read Sun Tzu's The Art of War and The Thirty-Six Stratagems. But of course they should have plenty of field experience, as ruperts that learned all they know from books tend to think everything goes exactly as planned.
If I'm fighting a hero whose family, friends, or loved ones I murdered, I will not taunt them by telling them "So-and-so begged me to spare his/her life". That's more than just flirting with death, that's raping him.
My Legion of Doom will never go out into battle with money or valuables in their possession, especially if they have a knack for dropping all of this when they die.
If my Legions of Doom manage to put one of the heroes in a state where he attacks his allies rather than them, they will be instructed not to attack said hero until all his friends are dead or he is no longer in said state. The same thing goes for if they manage to render one of them unconscious.
I will make use of a suit of animated armor or other robotic double, while I am somewhere else - preferably a bunker in the ass-end of Siberia or some other hellishly inhospitable place that would take a massive amount of preparation to get to.
Before I order the death of someone trying to reveal my dark secret, I will first consider the the level of deniability I have. If the revelation will only be believed by crazy conspiracy theorists, it would actually work to my advantage. However if the person planning to do this is the Hero, I will have them killed immediately, as they will inevitably get their hands on the evidence.
For similar reasons, if practical I will actively try to make myself one of the stock villains of crazy conspiracy theorists. Somebody planning to control the world will find that the perfect hiding place is within the Freemasons or Catholic Church.
I will also hire several assassins, equip them with poison daggers, and have them masquerade as prisoners. When the hero shows up to throw open the doors of the prison, their job will be to discretely stab him/her on the way out.
If the hero gives me a box that he claims contains an object I really want, I'll make sure the box isn't empty before I let him go.
If I make a bargain with anyone, I will do my best to actually hold up my end; lest it come back to bite me in the ass later. They only time I will backstab anyone is if I can kill everyone involved who could conceivably get back at me.
All minions (or at least as many as is practical) will be required to know basic first aid.
I will not give away my backstory or plans for world domination to the heroes. They can either figure them out on their own or die trying. I have a country/megacorp to run, I have no time to give exposition.
If my evil plan involves an ancient artifact of great power, I will take the time to study all information about it; if granting the hero a weapon capable of defeating me is the only way to obtain the artifact, I will pass it up for another artifact of similar power. In addition, I will look for an artifact that comes in one piece instead of several.
Before sending demonic shapeshifters to infiltrate the enemy, I will make sure that no animals or children are able to see through their disguises. They will also be trained to refrain from any kind of nonhuman behavior.
If an underling ever asks why I don't simply shoot the hero there and then, and I don't have reasonable answer, they may be right and shall be rewarded. But only after I simply shoot the hero, should it be possible to do that very soon.
If I learned that hero was raised in a certain orphanage that he still considers home, I will not send my legion to run it down. Instead, I will "offer" to fund the place and reorganize it - using my catchy theme song as the orphanage's anthem is the very first step.
If possible, I will avoid having me and myforces engage the hero in direct combat, as this usually won't end well. Whenever circumstances permit, I'll focus my efforts on assassinating the hero in as secretive and unexpected a manner as possible.
I will allow my henchmen to submit suggestions for possible weapon upgrades. Being on the field, they'll know what we need, and there's no sense letting the heroes exploit the same weakness over and over again.
If my evil plans involve immersing myself in the lifestream, I will first dip a toe in to see what happens. I will also wait an hour after eating to enter.
Failure will be punished by demotion and a round of brainwashing, rather than summary execution. Dead minions can't fight. Besides, brainwashing is fun!
When assembling teams, I will go through everyone's backstories to check for possible sources of conflict. If one of the potential members happens to blame another for the tragedy that ruined his life, they do not work together.
I will not use radiation or any radioactive materials in my lair; it is expensive enough to make specialized suits to resist radiation from Material X.
I will make sure factory by-products and mine tailings are properly disposed of. Living in the middle of Mordor, while great for atmosphere (figuratively of course), just screams "He's fuckin' evil!!!".
If I am running a minor dictatorship, I will not challenge a military superpower that could crush me easily.
If the idiot ball is a physical object, I will take steps to weaponize it. I will also take steps to contain the weapons-grade stupidity seeping out of the weapon. It just won't do to have minions forget that the skinny end is the one that hurts (or you keep the ring and throw the ball).
Whenever I temporarily leave my palace, I will make sure to put someone competent, but not too ambitious on the throne in my absence. I will make it clear that I'm coming home, and the kingdom is on loan, not a gift. And if he fucks it up, I'll fuck him up.
If I am ever bottled, I will ensure that I am either unconscious or have some kind of entertainment. Also if someone has released me demanding power, I will not kill them immediately; instead I will use their knowledge of the new time period, and give them a high position when I regain my authority.
If I am dying and I wish to continue my plot by digitizing my mind, the supercomputer better have access to the Internet or video games so I will not be bored in my confinement to a machine, and I can create a copy or escape elsewhere.
If I have to create a computer virus, I will also create an anti-malware program to circumvent the use of it on my own machinery.
Chimeras are a no-go. Even though it may seem interesting to mix and match creatures and play with life in general, they are still beasts and highly unpredictable.
If it becomes necessary to escape from my base when it's under attack, I will have my troops yell out sentences like "Prepare the escape pods", "Power up the teleport", or "Unlock that elevator to the center of the Earth". While they do this, I will silently walk out through the fire exit.
I will study the hero's abilities and use training, magic, or science to create henchmen who are able to counter certain attacks or have superpowers of their own. That way, I will have minions that are not only immune (or at the very least resistant) to the hero's attacks, but ones that will use the hero's own tricks against them as well.
I will regularly go on hunting trips and kill animals and monsters that are manageable within my current level of personal combat prowess. Not only will I get to broaden my horizons by doing something other than being an evil overlord, but I will get an influx of experience.
I will not use a door-lock system that deactivates when the hero kills everyone in the room. Instead, when s/he kills the last person, the room will collapse and/or become a vacuum.
I will not give my favorite/firstborn kid a cool theme name like "Mordryd" and my other kidsthrowaway names like "Jimmy". Given the amount of bickering evil children are prone to, Mordryd's probably gonna get a pen in the eye and the minions are gonna have to learn how to serve a guy named "Lord Jimmy" with a straight face.
I will make sure to keep my priorities in order: preserving my life and safety, maintaining my reign of terror, conducting my evil plans, and defeating the hero.
I call them "mooks", but really, they should all be highly-trained badasses.
Access to any important area of the base will require at least one of the following: a full palm scan, retinal scan, key card, voice recognition, or a 9-digit password. The scanners will be programmed to tell if someone is dead, in case the hero tries to carry a corpse to the scanner.
Alternatively, I will offer a bounty to any henchman who captures the Hero. The bounty will be offered to all who assist in this capture. I will however, pay in goods other than cold hard cash, to prevent inflation.
If I must offer a bounty, I will spread it evenly among the henchmen should one find him, as well as giving them a greater reward than a civilian. This has the added benefit of being a great campaign for henchmanship, increasing my evil army.
Or, I will tell my henchmen that once the hero is dead before me, they will all get a bonus this year. This will prevent the potential of squabbling and fighting each other for the rewards while ensuring they don't try and skimp me on the killing him part.
If my R&D team invents a bomb that can't be defused, I will get them to develop an ICBM that can't be re-targeted.
My fortress will have background music playing at all times. When the alarm rings and combat begins, a rock or metal soundtrack will play.
I will keep all new weapons top-secret until I develop counter-measures against them.
If I am accountable to a superior, and I have failed him, I will not blame my failure on my minions or colleagues, nor will I ask for a paycheck or a raise. This often leads to my execution, as a common trait of traitors is that they care more about themselves than their employer. I will instead take full responsibility for my failure.
If one lone scientist warns me that my latest plan will unleash horrifying forces upon me, I will put him on my top advisory committee instead of trying to discredit him.
Rather than trying to fulfill prophecies, I will stay the hell away from them!