Our software development department currently uses Subversion, and I create documentation using Frame. To me, Subversion is a version control system, and it ignores file types. So it's irrelevant if I'm saving .book or .fm files to a folder or directory in Subversion. I do maintain a separate documentation directory for files associated with each document, except for files that need to stay with the developers' files.
Subversion was a bit of a bear to learn -- it has some weird idiosyncrasies that I haven't seen in other versioning systems, but I also have a lot more control of creating directories and folder structures. Lea Galanter Lead Technical Editor and Writer Attenex, an FTI company