DocBook will be one way to write a guide, but I don't know about any CMS for it. I had my share in the work on PEAR, and so far I have always used a regular text editor to write / edit pages. I guess starting from scratch is harder.
If you need something more intuitive, try dokuwiki . It is quite small and lightweight and it works.
Also, keep in mind that phpdoc allows you to embed code samples, etc., so maybe look at this one too (for example: inline {@ example} ).
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