Erik Swenson of EMC uses VMware Workstation and a big snapshot tree to separate his Sharepoint projects. Link: SharePoint Branding & Design: Benefits of VMware Workstation for Branding.

I store them on an external drive and back it up frequently. This
allows me to take all of my work on the road or to any client site as
needed. As you can see from the screenshot on the left I normally start
all of my projects from a base vanilla image of SharePoint. … 

The great thing about VMware is that I can
always go back to any of my past projects and make edits or changes as
needed. Say for example you finished up a project about a month ago and
you are knee deep into another project. When all of a sudden you get an
email that there was this weird bug that needs to be fixed. All you
would have to do is save a snapshot of your current project and open up
the snapshot of the old project make the fix and you are done.