I've made some improvements to ApexDoc. Check out the writeup here: http://force-code.com/sfapexdoc/https://lucidwaresolutions.com/sfapexdoc/
In a nutshell, SfApexDoc:
- Parses javadoc-style comments and creates HTML documentation
- recognizes standard tags such as @description, @author, @date, @return, @param, @see.
- creates links to standard Apex types as well as your own classes
- includes full class, method, and property signatures - even those that span multiple lines.
I'm actively working on fixing issues and adding features, so please send me a note if you find problems.