I've rented under the following systems - some more fair than others:
Hobbs hours (i.e. engine start to shutdown)
Tacho hours
Takeoff to touchdown
Takeoff to touchdown plus 10 minutes
The last is perhaps the fairest, if your airfield is large - you pay for the straight taxy time but if you get stuck at the hold (I did 15 minutes at Cambridge recently) you aren't paying for it. The last two also have the advantage of not encouraging fast taxying. The second is nicest to the aircraft - it encourages you not to firewall the throttle all the time just to get there quicker, whereas the first is bad on all counts (people taxy fast then flog the aircraft to get there in the shortest time).
Tim