For some of the online help systems I've set up, I have found FAQ-O-Matic to be pretty helpfull, and really easy to setup. It's obviously more geared towards a faq style online help system.

Beyond that, in some other projects, I've used mysql coupled with perl, ala Open Interact, to handle simple text based additions to the help document, linking, etc. That way users don't have to know html or perl, they just have to be able to read and type into a form.

In the end though, it really depends on what sort of help system would be most benificial to you. I would really recommend searching around the net to find one that seems to fit the type of application you have and the type of questions that you seem to be getting, and beg the system administrator (or programmer) to hand over code.