I completely agree about with bkparikh about using micro-text. There are ways to include a "?" by an element which can raise a lightbox, etc. with a tip on how to use a function, when user clicks on the "?" sign or when user activates an element. I find this kind of help the most useful.
I would also consider creating a general video about your website / its purpose AND benefits. You could also create short videos for each major function which is not intuitive. Creating videos may be as easy as using adobe captivate: create a few screen shots of the function, then type scripts for each screen, then record the voice for each screen and finally compile a flash video. Upload it to youtube and then embed on your website.
If you get user emails and send out updates to them from time to time (say, on day 1, 3, 7, 30, etc.), then include a link to one of such videos in each email so that after x emails they have looked at all videos. Of course, not all of them watch videos or even open your emails, but it's an additional channel to get to your users.