Here it goes, then...
"-May I ask you something first?
-Shoot! Well, not literally, but ask away."

Looks like it's a bit tricky. Here's a hint: it's from a management-strategy game.

Damn, that sounds familiar. Since it's from a management-strategy game it's highly probable that I've heard something like that somewhere else, though, since I don't really play that kind of games. But still... meh, maybe someone else will know it, I'll stand by to see if I know the game when it's revealed.

A bit more help: the dialogue takes place between the protagonist and his actual workgiver.

well it WAS in Sam and Max season 2...

Not what I had in mind, and I haven't played that game, but if it's indeed so, you can take your turn.

Awww, I just watched LP of sam and max because of that and found out the quote is actually not the same at all, it's "Shoot!" "Ok" "Metaphorically." Oh well, it's not right I guess :D I DID hear that quote somewhere thou...

One last hint, if no one guesses it right in, say, 6 hours, Fenixp can post a new quote.
The hint: It's from a game on GOG.

The Settlers: Heritage of Kings? Probably a bad guess, but at least I've played that game so given that I think I've heard the quote somewhere this could make sense.

Pure stab in the dark, Republic: The Revolution?

Nope, neither guess was correct. The correct answer is Restaurant Empire. Armand asks Don Corleone the question and he is the one who gives the "Shoot! Well, not literally" answer, which is quite ironic.
As I said, Fenixp may take this turn (if he wishes).

So, Fenixp, do you wish to take this turn or pass it on to someone else?

Oh I'm sorry, didn't notice that :-) Well, someone take it I guess, can't think of anything

In that case, I'm posting a new quote in hopes it'll be easier. (A name will be omitted, indicated by [...], as that would be a dead giveaway.)
"-[...]! [...], can you hear me, my boy?
-Doctor, we're not getting through to him."

I'd probably need that giveaway :-P
I know I've heard the quote, but cannot place it at all.