Sometimes I need to merge two patches. I can apply them but often it is not convenient (coping, temporary files etc.). Is there a tool to merge patches (assuming they are not conflicting)?
If you manage patches often, then you may be interested in
quilt. I believe it has a patch combination feature.
See Quilt (software) for more info.
If you're interested in maintaining the source, you could put it into a version control system, add patches to it, and get the patches you want out of it.