Which configuration management tool is the best for FPGA designs, specifically Xilinx FPGA's programmed with VHDL and C for the embedded (microblaze) software?
I suggest CM tools that support version labeling and binary files. Most Software CM applications are fine with ASCII text files. They may just store a "difference" file rather than the entire file for updates.
My recommendations: PVCS, ClearCase and Subversion. DO NOT USE Microsoft SourceSafe. I don't like it because it only supports one label per revision.
I've seen Perforce and Subversion used in a couple of FPGA-intensive companies.
I have personally used Perforce, Subverion, git and ClearCase for FPGA projects. Since VHDL and C are just text files, any works fine. However be sure to capture the other project and contraint files and any libraries you use.
Also think about what to do with the outputs, e.g. log file and bitstreams. Both tend to be bit and the bitstreams are binaries.
We use Perforce, and its great. You can have your code that lives in Linux-land checked in side-by-side with your Specs and Docs that live in Windows-land. And you get branching, labels, etc.
I've seen everything from Clearcase to RCS used, and it is really all okay for this kind of thing. The important thing is to get a good set of check-in policies established for your group, and make sure they stick to it.
And have automated nightly regressions. That way, when someone breaks the rules, they can be identified and publicly shamed.