I use PHPFog to host my WordPress sites, but this issue is also relevant on other hosts. I develop locally, then I use the Git version control system to deploy my changes to PHPFog. When I push to my remote repo, the Git client on my webserver automatically pulls the latest files.
This works great for many things, but W3 Total Cache is not one of them. Every time I deploy changes to the server, I lose my W3 Total Cache settings. I can't include my settings in the code repository, because my local configuration is different from my server config (e.g., no APC Opcode Cache installed locally). But of course, if I put the W3TC files in my .gitignore file so they aren't deployed, then they are blown away on the server.
What approach do you recommend for deploying via Git or via VCS scripts like Capistrano or Vlad the Deployer?