A quick update in-between: I tried out OODoc, but I'm not sure whether it fits the bill. It's very module-oriented; I couldn't get it to include docs from my .pl files. I want to document the whole project, not just the classes. Still, I'll try to take further looks at it.

I have an important warning, though: OODoc can delete your files if you are not careful. The example given in the manpage will filter your source and replace the files with files without documentation. When I used that example, it replaced all my files with empty files :-( . Fortunately, I use Subversion, so that was not much of a problem. However, without a backup, these files would have been lost.

If you try out OODoc, make sure you work on a copy and use something like this

$doc->processFiles(
    source       => $distdir,
    workdir      => undef,
    version      => '0.1');
[download]

instead of the call to processFiles in the manpage until you know and understand what OODoc does. This will keep your source files intact, AFAIK.