Doctor Who Villain Rulebook

1. The Doctor lies. There is no reason for me to take the moral high ground in this regard. I too will lie, particularly during the bit when I am telling him my master plan. He's just going to figure it out anyway, I'm damn well not going to make it easy for him.
2. Should the Doctor give me the chance to renounce my evil ways (and he will) I will take him up on the offer, apologizing to all those I have oppressed and vowing to make amends. Then, when he gets in his TARDIS and leaves, I will go immediately back to whatever I was doing before he showed up.
3. If it becomes necessary to kill the Doctor, I will do so without hesitation. Preferably using some method that does not favor regeneration, such as charring him into ash with flamethrowers or dropping a piano on him.
4. If it becomes necessary to kill the Doctor's companions, I will do so without hesitation. They're more competent than they look, and if he does end up defeating me at least I'll be able to rub that in his face before I go down.
5. I will not let the Doctor talk.
6. I will not let the Doctor press buttons. Ideally I will not have any buttons that he can press in the first place. In a universe with voice print identification and bio-recognition software there's no excuse for getting defeated because the Doctor guessed your password.
7. Jobs done by biological henchmen will require a robot partner, and vice versa. This will act as a check and balance against the Doctor's usual tactics: the robot cannot be persuaded to join the Doctor's cause via ethical debate, and the organic cannot be overridden by technical means. This policy will be in effect over all employment grades, including guard duty, administration, and my personal harem.
8. I will invest in Deadlock Seals for absolutely everything. If I can afford a doomsday device, I can afford not to skimp on security. This includes the access panels on all the robots. Especially the robots in the harem.
9. I will never, ever, ever imprison the Doctor and his companions in the same cell block, let alone the same cell.
10. I will not imprison the Doctor in anything with a door. I will instead keep him in a 50-foot pit. 
11. My minions, henchmen, and administrators will not have identification cards or lanyards. Anyone attempting to gain access to anywhere but the cafeteria or the restrooms using a paper ID will be thrown into the 50-foot pit.
12. I will not try to out-science the Doctor. That never works and is utterly futile. Instead, I will keep on hand a variety of extremely low-tech alternatives for defeating him, such as a phalanx of archers wielding poison-tipped arrows, so that when he disables all of my technology I am not completely vulnerable.
13. I will not try to steal the TARDIS for it's technology. It's tempting, but I already have a doomsday device that I know how to use and there's no point crossing horses in mid-stream. Eyes on the prize. I will, however, have it couriered to the middle of the Pacific Ocean and dumped there. I will also keep on hand a number of standard British police boxes in random locations just to mess with him.
14. I will not form an alliance with the Daleks or the Cybermen just to defeat the Doctor. First, that's a tremendously stupid idea in general, and second, just look at their track record against him.
15. If possible, I will invest in a Raston Warrior Robot. Not even the Doctor ever beat that son of a bitch.
16. I will not let River Song kiss me under any circumstances.
17. If for some reason I am compelled to make a dramatic speech to the Doctor at some point, I will not bother trying to justify my actions or equivocating whatever horrendous things he has done. Those are rhetorical devices and I am above such petty bickering. Instead I will keep to the facts, pointing out that he always shows up uninvited and pokes his nose in other people's business and that's just plain inconsiderate and unwarranted.
18. Should I at some point capture the Doctor, he will be required to undergo the same thorough screenings as anyone boarding a standard commercial flight. Specifially, I will confiscate any and all items on his person that can be used as clever weapons. Which pretty much means any and all items on his person. Including his clothing. Especially his clothing. Especially if he is wearing a scarf.
19. At least one of my "advisers" will be someone who speaks in complete gibberish, to make the Doctor think his TARDIS translation function is on the fritz.
20. I will have an escape plan in case the Doctor defeats me. I am not an idiot. Putting all my eggs in one basket is just plain stupid. 

(Yes, of course it was inspired by the Evil Overlord List.)