Note that those three directories actually correspond to two complete perl installs, not three. /usr/lib/perl5/5.00503 contains the standard modules and other library files for an install perl5.005_03; /usr/local/lib/perl5/5.6.0 contains the standard library files for an install of perl5.6.0; and /usr/local/lib/perl5/site_perl contains site specific modules and is further divided into subdirectories for the different versions of Perl. For example:

% ls -F /usr/local/lib/perl5/site_perl/
5.005/  5.6.0/
[download]

Don't forget that these are just the library files; the binary files, usually in /usr/bin or /usr/local/bin, are also an important part of a perl install. :)