Ciao Ido,
every project has its dedicated tree that resembles the organization of a unix / dir, with bin, etc, lib, usr and var directories that contains all things related to it. Every project has an utility that backups everything on a separate removable hard drive, but this approach works for little projects; probably CVS would be a better choice.

I found some nodes related to this topic: Whats your development environment, Using CVS for revision control Keeping code up2date over multiple servers and perl development OS of choice. There was a nice discussion also on mod_perl mailing list, the subject was: (OTish) Version Control?

Ciao, Valerio