oooh, good one.
[to his minions:] “Kill them all, but leave <the hero> to me.”
Great additions so far! I cannot restrain myself from adding one more:
It is pity I must kill you now…
This is usually followed by 1 of two possible predicates:
…I would have prefered to stay and witness your demise!
…you might have joined us in our inevitable victory!
“Why am I surrounded by INCOMPETANTS!?” Usually said after killing four henchman in a row for no good reason.
“Seize him you fools! SEIZE HIM!”
“I could shoot you right now, but NO! There’s a better way to kill you!”
“Kill him, my Daughter!” “No Father! I…I love him! You’ll have to kill me first!”
“You’re TOO LATE! All I have to do is touch the hypernexus core, and I’ll absorb its power forever! I’ll be INVINCIBLE!” <touches core> “The POWER! The POWER! I am unstoppable! Wait, don’t touch that oscillation damper you fool! AAAAAAARRHG!” <villain explodes>
Also, a hero can never kill a villain directly. All villains must instead die by falling from a great height after attempting to backstab the hero.
And here’s a hero cliche: “Give me the girl and you can have the McGuffin.” Yeah, “the girl”. She has a name, you know. You’re in love with her. And now she’s “the girl”?
Variant:
“Kill them all, but leave the woman to me.”
That reminds me of a great line from the Penn and Teller movie Penn and Teller Get Killed (medicre movie but a few good laughs). After Penn and his love interest are captured by bad guys, Penn says, “Do what you want to the girl…just leave ME alone.”
We meet again!
“And I would have gotten away with it, if not for you meddling kids!” (sorry, I couldn’t resist.)
to Minion #1: “You have failed in your mission. Do you realize what the price of failure is?”
(taps hidden button, dispatches Minion #1 into a horrendous death-trap)
to Minion #2: “Now it is you’re job to dispose of <movie hero’s name>. Do. Not. Fail. Me.”
“Repent, Harlequin!” said the Ticktockman.
It is so cheesy classic SF, that it’s even the title of the short story.
Neither could I. 
You dare to defy ME?!
Bonus points if the villian refers to himself in the third person.
"You dare to defy Malgar the Destroyer?!
“We’re actually not all that different, you and I…”
Hopefully, and probably in a Joss Whedon production, the hero will reply by shooting the villain and then saying, “Sure we are. I haven’t been shot today.”
Inconceivable!
Which part of ‘cliche’ do you not understand?
“Home . . . I haff no home. Hanted . . . despised . . . liffing like an animal – de jongle is my home! But I vill show de vorld dat I can be its master. I shall perfect my own rice of pipple – a rice of atomic supermen vhich vill conquer de vorld!”
BWAH HAHAHAHAHAHAHA
If I ever write my own TV series I am SO using that 
Good job, Eve. Now let’s hear you call Boris Karloff a cocksucker.
::sadly loading my revolver::
I wish you hadn’t said that, Greenie.
“…in a different time and place, we could have been friends.”