The two options I consider for renting cars here are with www.easycar.com or www.auto-europe.com (who usually contract to Europcar which are great for rental extensions or changing return locations).
When dropping the car back at Geneva airport which also shares the two countries you must make sure you get back to the correct side's rental car return whereas Basel Mulhouse airport is so much smaller its less time consuming and not as much a problem finding where to go.
It was also handy another time because Basel Mulhouse is so close to the main access freeway that I was able to pull in and change my ticket with Easyjet so that I could have another day and continue on down to Geneva and fly to Berlin from there instead plus drop the car there!


