"so long as you make sure the files can't be executed"
Most formal theories of security are predicated on a logical expression of one or conditions. The problem with formal theories is they fail to anticipate behaviors outside the model. How do you make sure that the files cannot be executed?
Even Linux and Mac OS X/BSD machines occasionally come into contact with file systems that do not have execute permissions. Specifically, most removable flash media are formatted as FAT32.
Do your Linux machines automatically mount removable media?
Do you have WINE or another Windows compatibility framework installed?
If you answered yes to both these questions then congratulations: you too can be infected by Windows malware!
On the other hand if you virus-scan every file by default then you have less to worry about.
I disagree slightly with Hendrik. The main reason to check files for malware is to keep your own systems up and running efficiently. Then secondarily to keep your clients clean. If you lack the resources to operate, then fairly soon you won't have any. And virus scanning files is not really an onerous chore if you automate it.