The best way to travel between Jodhpur and Jaisalmer is by road.
The road is good and the trip takes about 4 1/2 hours.
Along the way, there are two good spots to stop for a break, conveniently located about half way.
Samsara Resort and Camp (Lunch from 12:00-15:00) Mains about $AUS 8 each, Lassi $AUS3
Manvar Resort and Desert Camp (Mains about $AUS7, Lassi about $AUS2)
Kathi rolls about $AUS6
Manvar Resort also has a lovely gift and book shop and nice accommodation (it also offers a desert luxury camp 7km away).