I was wandering around and guess what I found, an M.Sc. Thesis by Philip S. Anderson about the development of a UAV ground control station.
I haven't read it yet but it seens to be a really nice reference. He uses LabVIEW which by what I have seen is a very popular software among us(uhhh but I still a newbie).
What I think is a nice point of his project is that he actually built the system and put it on a van, so we can have a taste of what the military guys have :D
Just for the sake of knowledge, I'm attachig his work(am I infringing any law, copyright or anything like this?).
Ground Control Station.pdf