There is a court decision in the Canton of Aargau that, in the absence of an "etat des lieux" agreed upon by both parties when the lease started, the onus is on the landlord to prove that any damage that exists has been caused by you. Fairly difficult I would have thought.
This being said, it is difficult as an individual (and a foreigner at that) to deal with landlords and agents. My advice (if you haven't done it already), sign up immediately with your local branch of the Association des Locataires (ASLOCA) and get someone from the Association to come along and assist you when you give the place back. These people know what they are doing and know what tricks landlords use. We have used them in the past and they have always been worth their weight in gold. Normally costs about 150 Fr a time.
http://www.asloca.ch/
Good luck!!