With git it is easy to create one repository per project, and it almost always makes sense to do so. When using git-annex, what is the recommended setup?
Should one have a single annex containing all files, or is it recommended to create different repositories for things like 'photos', 'music', 'isos' ?
It makes sense to have separate repositories when you have well-defined uses for them.
I have a separate repository just for music and podcasts, which I can put various places where I have no need of the overhead of a tree of other files.
If you're using it for whatever arbitrary large files you accumulate, I find it's useful to have them in one repository. This way I can rearrange things as makes sense. It might make sense to have "photos" and "isos" as categories today, but next year you might prefer to move those under 2011/{photos,isos}. It would certainly make sense to have different repositories for home, work, etc.
How to split repositories up for a home directory is a general problem that the vcs-home project has surely considered at one time or another.