If you're on OSX you can do this:
http://mac.tutsplus.com/tutorials/productivity/how-to-tag-files-and-create-spotlight-comments-on-a-mac/
I don't know if Windows or Linux have a similar way of adding metadata to arbitrary files.
PS: there will be (or maybe is, can't remember when the option was added) a -wallet=<name> option to open up a different .dat file for the wallet.