Captain Janeway as Titania would command, though the queen of the fairies is not exactly the most sane CO you could have.
Her First Officer would be Riker as David Xanatos. Though how long he would remain first officer is debatable, considering that he's Xanatos.
Councilor Troi as Demona. Probably not the best choice of ship's councilor, what with all of the rampaging hate and evil.
Second Officer and ship operations go to Data as Puck. It may not be a good idea to entrust such an important position to a trickster elf, unless you want the ship a few thousand lightyears off course because he was bored.
At security and tactical, you have Worf as Coldstone (or part of him at any rate). Oddly enough, he'd be less likely to succumb to The Worf Effect due to being made of stone.
Chief engineer would go to Geordi as Anansi.
On a minor note, those of you familiar with the voice of Lexington may not spot him as the psychopathic Simon in Invasion America.
Casting Patrick Stewart as Seti in The Prince of Egypt might be considered a Double Subversion, as he initially acts like a typical "Patrick Stewart character" as a tough but loving father and authority figure deserving of respect. Then, in sharp opposition to the usual Patrick Stewart Speech, he gives a lecture to Moses justifying feeding thousands of Hebrew infants to the crocodiles. Even though the audience is likely to know of the almost-genocide from the Passover story, having Stewart in this role makes it shocking.
In a much less serious (and probably intentional) note, in American Dad!, Stewart was cast as Avery Bullock, Stan's often whimsical and bizarre boss.
Going even further, an episode of Family Guy had all the Next Gen actors reprising their roles...as themselves. Except that Stewart is the abusive father figure, Frakes is vapid, Dorn is the gentle guy, and Wheaton is the overeager chi...wait a second...
Similarly, Patrick Stewart being cast as the Yolkian king in The Adventures of Jimmy Neutron: Boy Genius qualifies under the comedic against-type casting as well, seeing how his overall character was somewhat comical in spite of his essentially being a sacrificing genocidal ruler.
The Prince of Egypt had this in spades: action hero-type Val Kilmer as Moses/God comes to mind.
Likewise, in Blade Runner, James Hong appears as a meek genetic engineer specializing in eyes.
Hong also played goofy Mr. Miyagi parodies in Balls of Fury and Totally Awesome.
Though his other roles may not fit, the decision to cast David Kaye as Optimus Prime in Transformers Animated raised many eyebrows among the fans, given that Kaye's usual role in previous Transformers series' has been Megatron.
The Wild Thornberrys had Tim Curry, he of the deliciously slimy and evil-sounding voice, playing the energetic, good-natured, and wholeheartedly lovable naturalist Nigel Thornberry.
Richard Steven Horvitz is usually known for playing goofy, loudmouthed characters who scream a lot such as Zim from Invader Zim, Dagget from The Angry Beavers, and Billy from The Grim Adventures of Billy & Mandy. However he played a serious role in Static Shock in which he played Jimmy Osgood, a shy, nerdy boy who was often bullied. Eventually, he loses it and tries to kill his tormentors with a gun, but he is stopped before he can do anything. The gun still goes off, though, and nearly kills Ritchie.
Horvitz also voiced the far more subdued and vastly more intelligent Grey Matter in the original Ben 10.
In an inverse to the David Kaye Transformers example listed above, Adler also voiced the villainous Starscream in the live-action movies. His best known Transformers role before that was as the considerably more heroic Aerialbot leader Silverbolt in the original cartoon.
Pamela Segal Adlon, usually known for voicing young boys or spunky or motherly women, voiced Luanne's violent, promiscuous, alcoholic, neglectful mother in an episode of King of the Hill.
While Transformers Animated's version of Waspinator, Wasp, would seem like his usual fare, you might be surprised. While Wasp is at least a little goofy, when he becomes Waspinator, he is instead a snarling, hulking monster.
His turn as the solemn, isolated (and kinda creepy) robot Fixit on Teen Titans was only further highlighted by his clearly in-type role as Mumbo the Amazing in the same episode.
And Sawada from Tekkon Kinkreet who is one of the most serious characters he's ever voiced, a no-nonsense, asexual detective.
Her role as Protoss Executor Selendis in Starcraft II isn't like the roles she usually plays either. Unlike the other roles she's done before, she really sounds dead serious and is devoid of her usual snark and sarcasm in this one.
There's also her turn as Blackarachia in Transformers Animated where aside from some sarcasm, she actually sounds quite serious and bitter.
Back in the 1980s, Jerry Orbach was known for playing on Broadway, as the "tough but fair" dad of Dirty Dancing, and playing mobsters... so what was he doing playing a Space Cowboy in Adventures of the Galaxy Rangers? Well, he had never done animation up until that point...
Her role as Hypnotized!Fluttershy in the Season 2 two-part opening also counts.
Tara Strong tends to voice good, even sweet characters - with Bubbles probably being one of the best examples. Of course, she also voiced Princess Clara and Toot - two characters about as far removed from Bubbles as humanly possible. Tara herself pointed out the trope when Drawn Together first premiered.
Continuing our Generator Rex theme, while John DiMaggio is no stranger for playing brawling adversaries in Hunter Cain, his first voice actor is someone who goes by the name of John Cena. Who's that? Oh...just a famous WWE wrestler who is pretty much Nice Character Nice Actor incarnate and an upstanding Face in the WWE.
Clarence Nash is famous for his many, many performances as Donald Duck. He also contributed to the vocal sounds of the bear from The Fox and the Hound.
Henry Winkler of Happy Days fame, in addition to his character Arthur Fonzarelli, usually voices suave characters whom everyone admires. However, in Sit Down, Shut Up, he voices the principal, Willard Deutschebog, who's a pathetic loser whom everyone mocks and abuses.