This might be a case of RTFM, but then I just don't see it: I was wondering if it is possible to have files added to a repository but at the same time keep them unversioned?
Currently I'm thinking of the .APS and .AWS files that AVR Studio creates. Especially the .AWS file gets modified whenever the project is opened in AVR Studio resulting in Subversion (and TortoiseSVN respectively, which is what I'm using as a frontend) to mark the checked out folder as modified. Adding the files to the ignore list keeps the files from being added to the repository at all, so when checking out into a new folder the AVR Studio project and workspace files are missing.
The second question would be: Which files do you have on the ignore list? Ignoring the .HEX and .EEP files as well as the .O and .D files seem natural since they are created at compile time. Any other ones?