Basic requests are:
We are thinking about using some kind of wiki engine, but it would need to use files for storage or have other means of "deployment" to customer and be easy to install/maintan. Also, it would have to be free / cheap (confluence is way too expensive)
Any suggestions?
Edit: I'm not looking for tools to document code, we have that covered using Sandcastle.
Although it may not answer all your requests, DokuWiki may be worth taking a look at.
As with other wikis, it has a simple syntax, and has version control to track revisions, generates table of contents, and a full-text search feature which can come handy for a help system.
You may want to evaluate the feature list to see if it will meet your needs.
Also, there seems to also be a good collection of avaialble plugins. Although I haven't used DokuWiki or its plugins, there seems to be plugins available for PDF export as well.