I've got all the Beast Wars episodes, so I'll see if I can find some memorable moments of Megatron's drawn-out "yes". (Going to take quite awhile, given that my memory is a bit rusty.)
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Edit: Yay... I finally got through them all. Here are the ones I selected. (Of course, a couple were previously mentioned, so credit where credit's due.)
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"Beast Wars, pt. 1"
Dinobot: "Their shields are down! Destroy them!"
Megatron: "Now where's the fun in that? A little torment, I'd think first, yes. Side gun!"
I chose this because it's the first instant of him using his trademark "yes". That and it helps flesh out his personality.
~*~*~*~
"Beast Wars, pt. 2"
Megatron: "Across the galaxy, it has come to this, Optimus Primal! Face to face, tooth to claw! Yeeess. Have you anything to say?"
Primal: "I'd say that's Prime. Let's do it!"
The "yes", IMO, isn't one of the better-sounding ones, but when put into context... you can decide.
~*~*~*~
"Chain of Command"
Megatron: "The day, and the probe, is yours, Optimus.
Yes. Just beware: not all aliens are beneficiant, after all."
Whoa. You can really hear the contempt in his voice.
~*~*~*~
"The Low Road"
Megatron: *swipes antidote from Blackarachnia* "No! Hmm. A bargaining chip should remain in play until the game is over, yess.."
The way he says it here always makes me chuckle for some reason.
Megatron: *growl* "This is certainly the most humiliating defeat of my entire career. Yes..." *groan*
I believe it speaks for itself. *lol*
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"Bad Spark"
Blackarachnia: "You! What are you doing here?!"
Tarantulas: "Hear you've got information I want."
Megatron: "Yess, let's hear it."
*lol* His tone of voice is perfect in this one.
~*~*~*~
"Code of Hero"
Megatron: "Yes. Yes! YES! Oh my crazed crustacean, yes!"
Sounds quite joyful. Not surprising, given that he only wants to change history.

~*~*~*~
"The Agenda, pt. 2"
Megatron: "Yess, you do that."
Ooh... talking down to Ravage. Nice.
~*~*~*~
"Feral Scream, pt. 1"
Megatron: *after TM2 Dinobot steps out* "Ahhh, yesss."
A good, short evil laugh of sorts.
~*~*~*~
"Go with the Flow"
[Can't really transcribe it, but Megatron does use a "yes" filled with exasperation while trying to get Una to work on his project. Heh heh.]
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