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We recommend using DocBook for writing your user documentation. The only exceptions are manpages for convenient executable references, and function references which are documented in the code.
Here are the recommended formats then, and some references to find out more information about them.
DocBook is just a stylesheet for SGML, which is a very general markup language. A good starting point for information is docbook.org.
Convenient for documenting Perl modules since Perl supports inline pod documentation. Run man perlpod for more information.
An inline Java source code documentation format. See Sun's Javadoc page for more information.
Write in present tense.
Organize your documentation into sections by who would want to read it (maintainers? sysadmins?). There should always be an Introduction that describes the basic functionality, scope, and modules in your program.