I also use POD to comment out blocks of code. I also never leave those blocks in for long (or at least strive not to). One trick i learned from merlyn is to be descriptive with the POD and use something like:

=for comment
 blah
 blah
 blah
=cut
[download]

But you are still going to interfere with any real POD your code contains - which is why i strive to remove unneeded code ASAP and let CVS handle the history (but i still leave phantom code from time out of false laziness).