Keep the plugins under git repositories. For your particular needs I think you could make a repository and use branches and git submodules (most of the plugins are under git anyways, so you can keep them up to date or use different versions even). A downside is that you can't use the Package Control, but you can use github to sync the setting across machines and workspaces.
If you don't want to lose the convenience of Package Control i think you can find its specific settings file (Package Control.sublime-setting – the user specific one) and branch it with git.
Update: I tried to use the settings option for ignored_packages with Package Control
in sublime-project but I couldn't get it to work at least on ST3.