One of the most commonly-used features in pro UAVs is point-and-click mission control in real time. Rather than just pre-planned missions or manually flying the UAV, operators can just click on a map and say "go here now".
Good news: we've now implemented this in APM. If you update to the latest Mission Planner and APM code, you can right-click on the map in the GCS and just select "Fly To Here". The UAV will fly there and loiter until you give it another command. We call this "Guided Mode". There are more commands coming in this mode soon, but the functionality is now built-in.
We'll be implementing this in ArduCopter 2 before it comes out of beta, too. Go Guided Mode!
[UPDATE] Team leader Doug Weibel explains how it works:
"Guided is a separate flight mode. If you enter it you will remain in it until you do something to change modes. So if you tell it to "go here now", once it arrives there it will loiter at the Guided waypoint till you tell it to do something else. Something else could either be going to another Guided waypoint (staying in Guided mode) or changing to some other flight mode. If you change to Auto your mission will resume where it left off."