A lot of the good ones were mentioned here... And some that would never work.

Cap and Bucky - The classic duo. I can't wait for a Bucky fig.

Venom and Spidey/Venom and Carnage - Venom and Spidey really hate working together, and hard to imagine, Venom and Carnage would never work together (they try to kill each other on sight).

Vision and Scarlet Witch - Very good combo in the comics and on the table.

Ant Man and Wasp - Makes for a more frustrating game than anything. Yellowjacket is more balanced.

Some more picks...

Doom and Doombot(s).

Black Bolt and Medusa.

Daredevil and Elektra.

Daredevil and Black Widow.

Daredevil and Echo.

Spidey and Daredevil.

Shadowcat and Lockheed.

Storm and Black Panther.

Kraven and Calypso.

Nimrod and Sentinel(s).

Did these two ever work together much in the actual comics?

No, they do not. While they have both been leaders of The Brotherhood, neither has been an active member at the same time. In the comics, Magneto is very political in his motivations while Mystique leans far more towards mercenary roles. I can't think of a single issue off-hand in which they've even met. I'm sure they probably have, but I don't know when that may have been.

Hey, let us not forget ...

Stan Lee & Steve Ditko
And
Stan Lee & Jack Kirby
And
Jack Kirby & Joe Simon

Thanks. I'm pretty sure that this is how things were but I haven't read much Marvel in the last six years or so, so they could have done something in that time. But it seems like, due to the movies and Evolution cartoon (and the Legends video games?), there are many people who seem to think that Mystique has been Magneto's right-hand-gal in the comics.

Off the top of my head of those who are in clix

Spidey and Human Torch
Spidey and Black Cat
Spidey and Daredevil
Spidey(Ultimate) and Kitty Pryde (Ultimate)
Spidey and Venom... sometimes...

Captain America and Nick Fury
Captain America and Falcon
Captain America and Black Widow

Wolverine and Nick Fury
Wolverine and Shadowcat/Kitty Pryde
Wolverine and Nightcrawler
Wolverine and Vindicator
Wolverine and Puck

Cable and Deadpool
Cable and Domino

Cloak and Dagger

Cyclops and Jean Grey/Phoenix
Cyclops and White Queen
Cyclops and Goblin Queen (well pre-her being the Goblin Queen...)

Luke Cage and Jessica Jones
Powerman and Iron Fist

Jessica Jones and Warbird

Daredevil and Electra
Daredevil and Black Widow

Scarlet Witch and Quicksilver
Scarlet Witch and Vision

Havok and Polaris
Havok and Goblin Queen

Nick Fury and Black Widow

Yellowjacket/Ant-man/Giantman and Wasp

Hawkeye and Mockingbird

Quicksilver and Crystal

Blackbolt and Medusa
Blackbolt and Crystal
Blackbolt and Lockjaw

Madrox and Multiple Man and Multiple Man and Multiple Man

Oh, thanks for that list. I was sort of looking for people in clix but I also wanted to know them not in clix

Iron Man - War Machine

Debbie and Dallas

peanut butter and jelly

franks and beans

Bud Palmer and Cindy Crawford

Batman dressed like Typhoid Mary and Daredevil