Pl/SQL Package Inline Documentation
I have used PlDoc and find it really good. I haven't used any other tools so can't compare. I found PlDoc did the basics well. I wanted some more advanced features so I built our own tool that added extensions to PlDoc for more tags. Also I don't just do documentation with it I also generate our package headers using some PlDoc tags (e.g @private).
I recommend you try PlDoc then tweak whatever doesn't meet your needs. It doesn't take that long to set up so its not a huge time investment to try it.
I've been using NaturalDocs for a few years now and have found it easy to install and use.It's pretty much like JavaDocs and supports multiple languages although I've only used it with PL/SQL.Very configurable although I've not found it necessary to fiddle with that.