5. The arms race will never work in your advantage.
As soon as you come up with a weapon that the heroes can not stand up to their tech team will come up with something even better that you can't stand up to. The trick is, don't go bigger, go different. Awesome is hereby defined as someone who leads the heroes through a vast dungeon filled with fire and lava, then after they've got enough energy resistance to make themselves practically immune to fire, hits them with LIGHTNING for instant death.
4. The size of the force against you is inversely proportionate to how scared you should be.
If Saddam Hussein could fuck with the UN for years there's no reason to call a red alert when they come after you. Movies and real life have taught us that the heriarchy of effectiveness goes from Masked Vigilante to Secret Agent to Navy Seal to Suspended Officer to Detroit PD to LAPD to FBI. By the time you've got the UN or Interpol involved an old woman in a wheelchair with a cap gun is a more formidable opponent. The true threat to you is not the army, but a small force infiltrating your compound and killing you in your sleep.
With that in mind, let's work on your security. Ventilation systems should be too small for a human to fit through. The door should not be guarded by idiots who let in anyone wearing the right uniform, but a DNA scanner which can determine 100% who is and isn't one of your guys. Finally, security cameras should be everywhere in your compound. They should face the correct way at all times and should be shielded against electromagnetism and whatever other clever devices the enemy has.
3. You're better off as a human.
Be it Voltron, Power Rangers, or any other show where humanoid villains assume giant monster forms, it's always the same. They're almost always winning when they decide to take giant monster form. At that point the fight usually lasts about 30 more seconds before the villain's horrifyingly brutal death.
Here's another thought. When Voltron Force assembles, or the Power Rangers form the Megazord, that's when you get OUT of giant form and then fly your tiny ass over there, get inside, and blow them up with a nuclear bomb or something. Those giant robots are packed with weapons that can kill giant enemies, but nothing against tiny ones. Seriously, haven't you seen Star Wars? Also, they probably won't even look for tiny you. They'll be looking around saying "Stay tight, gang. He must've turned invisible. He's right nearby, I can smell it! Hey, what's this? He's on the Megazo--" BANG!
My realizing this does, however, make me exactly as smart as the Green Ranger. One of the few good villains out there.
2. Your underlings are not mooks.
I know it might not be evil enough, but your underlings would be more loyal if you didn't view them as expendable. Also, it would be cheaper and more effective to keep one group of hirelings kept up, healthy, well-equipped, and well-trained, rather than just hiring on meat puppets by the truckload. Replacing your workforce with robots or zombies may solve the first problem (loyalty), but it exacerbates the second. Zombies are known to be weak and easily burned. Also, they stink and tend to rot and fall apart. Well preserved, a zombie might last you a month. And robots? The construction of one robot alone is the same as a year's upkeep for 100 humans. And that's not even counting the upkeep for said robot which is even more than a person would cost.
Also, on the topic of Star Wars...how are all the Storm Troopers terrible shots? Really, how? THEY'RE CLONES. They're genetically engineered in a lab. You can give them ANY TRAITS YOU WANT and you chose to make them completely skilless with the only weapon you give them? That's RETARDED. (Also, aren't they cloned from the best shot in the entire galaxy?)
1. When your enemy has racked up a monstrous body count before you, a non-violent resolution is usually in order.
Maybe Superman and Batman have codes against killing, but when you're going up against a foe who has a history of all his villains dying in humiliating and ironic ways, you don't want to invoke the fight-to-the-finish unless...well, never. You WILL DIE. If you're nice enough not to actively seek the hero's death he might return the favor. I'd mention something about movie action heroes like Rambo or Steven Seagal (I use the actor's name because I can't think of any of his characters' names and let's face it, they're all the same anyway) but they'll probably kill you anyway.
I'd actually like to see a plotline in a strip like Dick Tracy or Phantom where the villain, rather than fighting to the death, just suddenly dropped his gun and surrendered, just so I could watch the hero stare dumbfounded. The bad guy could probably just escape right there as the hero tried desperately to figure out what to do in this situation.