Not to be overly flip, but the best way to document Perl code is the same way as you would document code in any other language.
As for specific tools, I use a mix of standard inline comments, pod for larger chunks of documentation where a format similar to man is appropriate, and TeX as a final fallback for documents that need to be more freeform. (And, in the spirit of "same as any other language", yes, I do use pod for documenting non-Perl code as well.)
