Alot of good ones in here, but you're missing the swagger!
You know, the classic strut that the villain does once he's defeated his enemy. And it's multi-purposeful! Swagger after felling a hero, for looking cool in your base, or for scaring pedestrians out of your way on the street. 
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and last but not least...pulling out hair in frustration. Grab head and shake it back and forth screaming.
;headache - The villain stands with his head down, thumb and index finger pinching the bridge of his nose.
;givemeaminute - Villain holds up his right index finger, as if saying, "Give me a minute," and then turns away.
;boo - Various cat calls, thumbs-down, general dismissiveness.
;shootme - Mock shooting himself in his head with his finger-gun.
we need a world's smallest violin of some sort
You know a crying me a river sort of thing
Many good ones so far. Don't forget the Superman 2 "KNEEL before Zod!" imperious point to the ground, especially if it could be combined with the appropriate phrase.
/yawn -- Villain yawns in boredom at the hero's futile attempts to escape his doom! Something like the arms crossed, one hand stroking chin emote, but with a bored yawn and hand waving over his mouth instead.
Pelvic Thrust. That's so mandatory I'm surprized it isn't already in the game :P
/e straight jacket- just that
/e shovel, pulls out a shovel, points at a hero and begins to dig a grave
/cuffme (holds out wrists as if awaiting handcuffs)
26) fuming mad (literally in the case of fumes surrounding the villain - sort of a dry-ice entrance - or emerging from head)
39) palms up, widening to open arms - "Is this/that all you got?"
I would like to (with big smile) lean forward slightly and slowly bring my index finger to my lips saying "Shhhhh" to sooth my victims tears.
Laughing that turns into a fit of coughing. Those people with the old man face should act like old men.
a break emote where the character puts both fists together infront of him and then makes a 'twig snapping' motion.
If I high level hero challanges me to a fight, I want to stop for a sec, look at my watch, and then shrug my shoulders. Sorry, gotta go! Dentist appointment! Just the watch and the shrug would be the emote...if that wasn't clear.
/em thememusic (a villain's got to have creepy entrance music!)
plantbomb- plants one of those bomb-looking clickys. If nobody clicks it, it could blow up,(no damage of course) leaving an ugly scortch mark on the terrain that fades slowly with time.
Alot of good ones in here, but you're missing the swagger!
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I dig all of these... whew that was alot of reading 
Shakes fist while saying "And I would've gotten away with it too, if not for those pesky kids!"
Scorus
Have the villian do the mock - Oh I am so scared look and say, "My Grandmother hits harder than you do."
Cigar crushed on someones chest.
Don't know if these have been ssugggested. Such a long and good thread.
- The villian needs to be able to turn areound, bend over and moon someone and/or pat his/her butt (i.e. kiss this!).
- Or a Rosanne Barr grabbing of the nards.
- Or the villian can pick his/her nose, look around and either eat it or pretend to wipe it on their constume.
- Could also have a fart sound then the villian has an expression of eembarrasment and/or points to someone else and says "He/She did it!".
- Finally the villan should bea able to emote sucking their thumb.
How about ripping hair out in frustration?
Or a sneaking one, they press their back up an imaginary wall and sneak along it a few feet.
Also: A begging one, for when a hero is about to finish them off!
The classic "slide hand across throat" throat slitting motion would be cool.
1. One hand bent into a raised, half-claw while realizing dreams of villainous grandeur and the other hand clasping the hem of his/her cloak.
2. A dismissive, "you are inconsequential" wave, reserved for minions and petty heroes.
I would like something for the master villains and their high tech lairs with an emote of taking out a board and a pointer stick to show of their master plan and badgering to the hero on how the villain plans to destroy or rob or whatever giving a chance for the hero to get away (although you wouldn't want that to happen, it would make everything more exciting as in another emote in saying "Get Him/HER!" Sending minions of liutenants to run after the fleeing foe.
Another is that if the hero for whatever reason runs away the villain can wave the finger back and forth saying "Nu uh nuh Not so fast!" and caging the hero in some box or whatever.
if you want an evil clown, make a pie throwing emote.
Cabbage Patch dance
The wwf DX "suck it" pose.
definetly smoke coming out of a cigar, if you can get one.
The kneck slice, where you run your thumb along your neck signifying you'll either slit their throat or cut their head off.
I want the pose where the villain stands with his feet almost three times the width of his shoulders with his arms crossed of fists at waist. Great villain campiness.
Oh, and how about a fetal position for when the megalomaniacal supervillians plans are completely upturned and his mind snaps.
Maybe a donning of the (temporary) black cowboy hat?
Perhaps the one or two-handed messaging of the scalp to facilitate the villain's optimal cognition
How about the 'point the finger at everybody else, it's not my fault' emote?
Gotta have the universal 'it's about the money' emote, rubbing one hand's thumb and fingers together.
How about taking out a hundred dollar bill and using it to light a cigar?
/e flask
/e smokepellet (where villains can throw down some smoke and run; purely visual, but it'd be fun to watch)
/e trip (trips the next passer-by)
/e smoke (cigarette or something)
/e playdead (really dramatic, thespian death. very overdone)
/e disgust (when all my minions die at once, i want my villain to shake his head and bury it in one of his hands. like "why do i pay them?")
/e freeze (villain freezes in action and doesn't move an inch. or poses like he was running and time stopped around him)
and if it's possible, i want a 'point and laugh" for when my archenemy dies.
;ninja: A ninja appears adjacent to the villain, accepts some instructions, then vanishes. Could also work for a butler, igor...
;swirlwine: The villain pulls out a wine glass full of some red liquid, cupping the bowl in his fingers, and swirls it casually.
;chart: The villain pulls an easel and pointer out of nowhere and indicates his evil plans.
;babes or ;hunks: The villain snaps his fingers and scantily clad npcs of the appropriate sex appear and drape themselves upon him/her/it.
Story Arcs I created:
Every Rose: (#17702) Villainous vs Legacy Chain. Forget Arachnos, join the CoT!
Cosplay Madness!: (#3643) Neutral vs Custom Foes. Heroes at a pop culture convention!
Kiss Hello Goodbye: (#156389) Heroic vs Custom Foes. Film Noir/Hardboiled detective adventure!
;origami
Avatar makes an origami crane. Laughs with glee and stares at it until emote stance broken.
Just one word;
MONOLOGUE
thank you.
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"Thank you for encouraging my behavior."
~Bobcat Golthwaite
1) You need to be able to pull out a cell phone/walkie-talkie; speak on it for a short duration; then pop it back into your coat--giving orders to minions.
2) This isn't really an emote, but rather just something that should be in place...NO civilians should be able to push you; and if they do, you should be able to push them on the ground, mug them, or...well, just attack them.
3) One fleeing method/emote could be Dr. Lizardo's hunched over, fleeing-hobble from "Adventures of Buckaroo Bonzai". "Laugh while you can, Monkey-Boy!"
4) While this also isn't much of an emote, but rather character design, it would be cool to have an old man in a evil wheelchair...aka: David Lo Pan from "Big Trouble in Little China".
5) Pulled straight from "Blade Runner", the "angelic" stance Roy Batty does at the end, with dove in hand...showing that villains are products of their society.
6) From "Blue Velvet", need to pull out a nitrous mask and breathe heavily...possibly be able to say the quote, but that depends upon the rating of the game.
7) Basicly any emote Dr. Frankenfurter does from "Rocky Horror"
8) From "Time Bandits", be able to point finger at a minion, and blow him up; then hold finger up and say, "That's a good point."
9) Pull out a small, hand-held detonator (whether or not it's wired to an explosive is not important), for that dramatic escape where the hero is contemplating the choices.
Remember Citadel Station!
"Glory to the Many!"
Richter Wallens - lvl 35 ill/kin controller
MkII Mediziner - lvl 34 emp/rad defender
Need a salute of some sort... Not the american salute like what we have... Villains should have like 3 different kinds so they can choose.
Salute 1: Fist to chest
Salute 2: Arm bends at elbow and shows the back of hand.
Salute 3: Fist to chest, then to the sky (might seem a little nazish so its a maybe)
/em Pelvic Thrust 
Females: /em Slap (walks up to target and procedes to slap it) (must also make it so this cant be abused)
/em Gslap (takes off glove (any) and slaps the hero like the female one (A Duel it is!)
/em Lookatwatch (Just to look impatient)
/em summon (creates a green fire like the COT)
Don't think anyone has posted this, but a fake death emote would be very cool and very villain-ish!
Definately need some overly dramatic looking emotes. Think The MONARCH! or Doc Orpheous from Venture Bros
Lets see.. what else.. Insane laughing, maybe some nervous twitches...
What if the dastardly villain pulls a small, defenseless puppy out of his pocket (or behind him, or whatever), and punts it for a good 20 yards. Slam dunking a kitten would also be acceptable.
Puppy punting and choke slamming citizens would make me one happy villian.
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What if the dastardly villain pulls a small, defenseless puppy out of his pocket (or behind him, or whatever), and punts it for a good 20 yards. Slam dunking a kitten would also be acceptable.
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I just don't think evil enough.
The 'whip a citizen from behind you and hold him/her in front of you like a shield while you back off' emote
On another note, since we're all talking about emotes I really feel we need a /e dance, hammertime
Come on, imagine that. A bunch of heroes going "Stop. Hammer time.."