If your project is of any significant size, you should probably be shipping three different kinds of documentation: man pages as reference material, a tutorial manual, and a FAQ (Frequently Asked Questions) list. You should have a website as well, to serve as a central point of distribution (see the guidelines on communication in Chapter 19).
Huge man pages are viewed with some disfavor; navigation within them can be difficult. If yours are getting large, consider writing a reference manual, with the man page(s) giving a quick summary, pointers into the reference manual, and details of how the program(s) are invoked.
In your source code, include the standard metainformation files described in the Chapter 19 section on open-source release practices, such as README. Even if your code is going to be proprietary, these are Unix conventions and future maintainers coming from a Unix background will come up to speed faster if the conventions are followed.
Your man pages should be command references in the traditional Unix style for the traditional Unix audience. The tutorial manual should be long-form documentation for nontechnical users. And the FAQ should be an evolving resource that grows as your software support group learns what the frequent questions are and how to answer them.
There are more specific habits you should adopt if you want to get a little ahead of mid-2003's practice:
Maintain your document masters in XML-DocBook. Even your man pages can be DocBook RefEntry documents. There is a very good HOWTO on writing manual pages that explains the sections and organization your users will expect to see.
Ship the XML masters. Also, in case your users' systems don't have xmlto(1) ship the troff sources that you get by running xmlto man on your masters. Your software distribution's installation procedure should install those in the normal way, but direct people to the XML files if they want to write or edit documentation.
Make your project's installation package ScrollKeeper-ready.
Generate XHTML from your masters (with xmlto xhtml) and make it available from your project's Web page.