1) Captain America - Thor : This combination is an overly used one, yet very powerful, if you use a Generalist Agent and defensive Captain America (Chaotic Iso 8 work very well on him)
2) Captain America - Scarlet Witch : This is also an overly used combo, one of the most powerful in the game if you use your heroes right. WWII Captain America is recommended. He will protect Scarlet Witch while SW is preparing the Probability field and buffing your allies with Chaos Shield.
3) Colossus - Emma Frost : I used this team when I first recruited Emma Frost : Use Modern Colossus (I use his as a scrapper in order to last longer against blasters, who kill bruisers easily), put Sturdy Iso 8s on him and use Emma Frost offensively.
4) Black Widow - Captain America : this is a great combo to counter Scarlet Witch and Captain America. I use this team with Generalist Agent, Offensive Avengers Widow and Chaotic Avengers Captain. It is a good team especially with the Avengers costume because of the coordinated attacks and cooperative defenses.
5) Bruiser Sif - Wolverine : Those heroes are a good pair, if they are used properly. Sif uses Leaping Slash first, which leaves target vulnerable to slashing attacks and Wolverine becomes Stronger against that enemy, since all his offensive attacks are slashing.
6) Phoenix - Kitty Pryde : This team is a very good one. If Phoenix buffs Kitty Pryde with Mind Link while Kitty is phased, she will protect and dodge all the incoming attacks because of the Phased buff. Untill Phased is gone, Kitty is the best tank in the game.
7) Mockingbird - Captain America : Mockingbird is a very nice offensive hero, and if she is under the protect of Captain America, she will last longer in the battle. Unfortunately she isn't available anymore so this combination is rarely used.
8) Emma Frost - Thor : (Infiltrator Agent, Quantum Jumper, Knight, GG, and Pawn): Using QJ (Agent) and GG for Crit next hit for Thor after that Inspire Bravery (Thor) then Unlock Potential (EF)
End with Summon Thunder (Thor) If they don't have WWII CA then all should be overkill in one hit. If they do, CA down then just use EF's L1 on stronger ones and you know what to do for the rest.
9) Emma Frost - Scarlet Witch : Infiltrator/Tactician Agent (Knight, Pawn, Curative Reach / DD, Svalinn Defender): Agent just for tank and counter-attack with Knight, buff with Pawn then Svalinn Defender. Use EF's L1 to take down the tanker then SW to unbuff them.