I recently wrote a few scripts to generate HTML documentation from our library and scripts.
I was surprised how hard it was to get links from one page to another to target methods correctly. It's not really suprising though, since POD knows nothing about methods.
In the end, I used scripts based on the Krang doc building tools to munge the output of pod2html. I took links to #sections and made them #item_section since we have a convention of putting methods in =over/=back lists.
Likely to break, but works for now.