For deploying scripts and sorting out the #! line, there's a trick:

perl -MExtUtils::MY -e 'MY->fixin(@ARGV)' *.pl
[download]

This is the same mechanism that make install uses for scripts: it will set the perl path to the right thing on Unix, and run pl2bat on Windows.

Concerning portability in general, you might be interested in the slides for a talk I have given on portability at two YAPCs.