Which two teams have you personally teamed up that most people probably haven't, and how did you do it? (Thought this would be a good idea to get some ideas flowing)

I have teamed up a lot...but mostly for synergies so they probably have all been done by many others
Spider-Friends Morlocks-Evasion Beatdown/Stall
Spider-Friends X-Men Longshot/Madame Web/Out of Combat stun combo
X-Men/Brotherhood New Brotherhood Beats w/ Quicksilver finish
Heralds/Doom- Amazing synergy probably my best team up deck and one of my best decks.
Heralds/Spider-Friends-Stall/Control to Galactus
Teen Titans/Avengers-Team Attack deck
X-Men/Sentinels Multiple Man/Longshot/Wild Sents

Oooh... I've got a bunch of ideas for this coming up on Monday. I'm really looking for some sort of Substitute-focused team-up right now... DE/MD seems interesting, but I haven't totally worked it out yet.

Negative Zone and Fearsome Five.

It worked about as well as you'd expect.

Manhunter / Sentinel

Seems pretty intuitive, but I have yet to see it discussed or even mentioned.

(Edit - When it worked it was quite fun; unfortunately those times were further between than I might have liked.)

Injustice gang / Future foes (Yeah Ive been to the edge and jumped right off)

JSA / Anti-Matter BIG weanies.
Qwardian watchdog + Terriffics + T-Spheres = 11/11 1drop. (cloned with changling so you end up with 4)

Shadowpact / Squadron Supreme (also known as Suicide hotline)

Morlocks/Villains United.

Dr. Light + Storm + 4 Join Us or Dies = free Plague, Angel Dust, etc. Massive weenie attack. Science Spire them back for more cards. Talia on 5, put 'em back out.

No, it didn't work. Thanks for asking.

Oh, I had a REALLY fun New Gods/Heralds of Galactus deck that aimed to use Takion <> Highfather on 6 and then again on 8 (with some help from Silver Surfer) to speed up to Dark Phoenix on 10.

I teamed up Squadron Supreme w/ Emerald Enemies about a week after the Avengers Pre-Release. The thought of trying to have no hand and no resources while still trying to win made me giggle. Obviously, there weren't many wins with that deck.

I'm currently looking at Fearsome Five and Wild Pack. Mostly because Shimmer can be quite silly, and teaming up two "sub teams" seems like fun.

Checkmate/JLI. its fun.

Checkmate and....
Antimatter aggro
New Gods stall
Morlocks stall
Fearsome Five (location burn 4 drop)

Also, tried a few other strange teams, sometimes it worked out...
Masters of Evil/Teen Titans - was trying to break Jericho and substitute, but unfortunately, KO your 3 drop and not playing a 5 drop to steal their 5 drop wasn't as devasting as I thought in my head.

Villians United/Injustice Gang - plot twist denial and combat control with all the exhaust effects and JUOD combos. Just not enough to make it work reliably.

Wild Pack/Injustice Gang army - had so much potential but War Paint did fine without wild pack characters or team-ups...

Negative Zone and League of Assassins. eventually added Marvel Knights for stability. it was really fun.

also, not long after DOR came out i posted, before i'd heard anyone else use the name, a deck called "Evil Medical School" on decktech.net teaming up doom and fearsome five, leading up to a gamma bomb on 8 and dr light boosted on 9.

JLI/Avengers team attack, Squadron Supreme/Future Foes Discard and Marvel Knights/Revenge Squad for Midnight Sons use are 3 of the more unusual team-ups I've tried.

In the early days of the game (MOR, DOR, and MSM starter) I teamed up Fantastic Four and Syndicate for the synergy between 7 Drop Doc Oc, and 8 Drop Invisible Woman, booyah. I also made Negative Zone/X-Men, and a Brotherhood/Sentinel Lost City deck. Janky, janky days.

Future Foes/Brotherhood - Fatal Five and Freedom Force
Future Foes/Squadron - trying to abuse Peace in our Time
B.P.R.D. / JLA - equipment beats
JLA/Heralds - Red Shift with Teleport Tube

Many others that worked even worse.
Currently working on S6/Underworld, but saw a list today that's better than what i've got