Rule #1: Be courteous. I err on the side of being too courteous, perhaps, but that's my rule and it has served me well.
Example of someone not being courteous: I was discussing the courtesy car at a Class D airport FBO and they told me that some guy in the past had driven it 100 miles away to another airport, parked it in the paid parking lot, and simply left it there. They had to fly down and pay parking fees to get it back. That guy was NOT courteous.
Example of being too courteous: I diverted to a Class E airport after hours due to weather. There was a sign in the FBO that said the courtesy car was limited to 2 hours. I was spending the night so I spent $70 each way on a taxi to a hotel. When we got back to the FBO to finish our trip home in the morning, the people there told me that I should have called and they would have been glad for me to take the car overnight as long as they knew who had it.
At staffed FBOs, I ask if they have a car available (since it could already be spoken for by the time I arrive) and tell them when I expect to be back with it. They've never been worried about anything up to 4 hours or so, or an overnight when we diverted for weather and asked politely. At unstaffed FBOs, I try to find an obvious place to write down who has the car and how to reach me so if anyone comes in and absolutely needs it they can get in touch with me and I can bring it back for them.