What books are used by the Denver missions?
As far as I can guess, it seems like just SR4a, but we are still preparing to start our first SR game so I haven't looked at any of the missions.
I would love for them to use other books like arsenal and unwired so that our GM would allow them.

(I'm not asking what is allowed for official play, I know that, but what the missions themselves use(npcs and such))

The missions themselves only require SR4(a).

A lot of the Denver arc was written before many of the Core books for SR4 were released, and before many players could be expected to own or have access to some of those books. So they generally weren't used much. I'm not sure if they started utilizing them toward the end of Denver or not, as I never had the chance to play through those.

New York, on the other hand, makes a bit more use of them.

Bull