The Marvel Universe has a number of organizations that deal with different threats the world faces:

S.H.I.E.L.D. Deals with superhuman terrorists

S.W.O.R.D. Deals with alien threats

W.A.N.D. Deals with threats of a magical nature

T.I.M.E. Deals with temporal anomalies and time displaced threats

A.R.M.O.R. Deals with threats from alternate universes and dimensions

If you could make your own agency what would you call it and what would they specialize in fighting? Also what would be your cool HQ?

Ok I'l start:

A.T.O.M.- Affirmative Taskforce fOr Mutants (the names a work in progress, anybody think of something better that fits in ATOM?)

Lead by Director Nathan Summers AKA Cable, A.T.O.M deals with threats to Mutant stability and way of life, it's basically X-Force but with a massive upgrade and the HQ will be called Providence, rebuilt where Utopia used to be.

S.M.U.G. (The Strategic Ministry for dealing with Unctuous Goody-goodies). Deals with superheroes who are sanctimonious assholes. Mostly fights Iron Man, Captain America, Wolverine, Cyclops, Beast and Mr. Fantastic. Headquarters would be an underground base underneath San Fransisco.

LOL that's great.

S.P.I.D.E.R (Superior Program of Idea Driven Emergency Response)

Basically SpOck's goons responding to emergencies around NY.