Just a couple of short points.

First up: use your own documentation.
Try and use every feature as you've described it in the docs - I find I sometimes miss a piece of functionality in the docs (or even the code) if I'm in a hurry.
Have your colleagues/friends use the code using only the documentation, not verbal tips :-)

Depending on the complexity of the system (and the skill of the document's author), I've also found that a number of increasingly more detailed sections can be of great help. I don't want to have to read the whole 100 pages of the document to know how enough about how the system works to begin to follow it.
Good diagrams can also help - a picture says a thousand words...

As already mentioned, good examples are one of the most useful pieces of the whole document.
Showing how to solve the problem the code was written for using an example or two can make sense of several pages of more in-depth options, methods or sub-commands.

Update: Oh, and if no-one ever uses the docs, best find out why: either you have built the best piece of software ever, or the docs are rubbish :-)

BazB