There's also a couple of other ways I've always found to be helpful in debugging perl scripts, especially since I mostly work in a web environment.

Setting a scalar (say $debug) to 1 or 0 at function call and having your print functions conditional on $debug being true.

( print "I'm here" if $debug ). Better yet, writing your own debug function that listens to some higher-level variable is also a great way to do it.

I also recommend the very nifty Smart::Comments from CPAN, which allows you to use specially formated # comments based on conditions, printed to the buffer.