This is actually a subset of the third part in our non-profit SEO series, building external links, but I thought it deserved its own entry. If you've got patience, it's a good idea to submit your site to the Open Directory Project (DMOZ) and perhaps other directories -- human edited compilations of categorized sites.
A number of the big directories seem to have stopped taking free submissions completely (e.g. Yahoo) and since we're focusing primarily on "organic" search engine optimization, we'll focus on the free options. Of these, DMOZ is the biggest and the most important. Google's directory (and a number of other directories) are populated directly from the DMOZ listings, and Google tends to give a pretty good bump in the rankings to sites that are listed in DMOZ.
Essentially, all you have to do is visit DMOZ (dmoz.org), navigate to the appropriate category for your site, and click on "Submit a site" in the top menu bar. The page that loads will have instructions for each field. Try to follow them as closely as possible or you risk your site being rejected. The only field that gives you some creative license is the 25 - 30 word description, so choose your keywords wisely and craft a compelling, accurate description.
Since each category is managed by a volunteer editor, it may take some time for your submission to be processed. In fact, if there is no editor currently, your submission may be in an indefinite limbo. But it's worth taking some time to put the submission together and following up after three weeks or so if you haven't seen your site listing come active.
We've done a little exploring into alternate directories that offer free listings to non-profits, and there are a few that do so. We had a good experience with Go Guides (goguides.org), who gave us two free listings after I asked. (It doesn't seem to be officially listed, but I used the contact form to ask if they gave non-profits free listing, and they were very friendly and accommodating).
There is also another genre of "directory" which is essentially a variation on a link farm, asking for return links for a free non-profit listing. I experimented with one of these but was unimpressed -- they asked for a quality return link but the listing they provided was deeply buried and obfuscated by javascript, essentially neutralizing any search engine benefit your site would get from it. I recommend not entering into any "link for link" exchanges with directories such as this and saving your outbound links for relevant related organizations or issues.
As changes we've made with our search engine optimization strategy begin to propagate in the search engines, we've continued to crawl up in the rankings for our targetted keyword phrase, "non profit web design." Breaking into the first page seemed to take a little longer and require a little more effort, but as of right now we are in 8th place (out of 24,200,000 results on Google). There seems to be more turbulence in the rankings at this level -- one day recently we were in 6th place, one day we were bumped off the first page again.
We had a great DMOZ submission experience -- after three weeks or so, I contacted the editor of our category and he was very responsive and helpful and told us when he expected to get to our submission based on how far down the queue we were. We were added to list almost exactly when he told me he expected to process the submission. At the moment, we are listed in DMOZ (in this category), but Google's own copy of that folder has not yet updated in their directory (here). Perhaps we'll get an additional boost when Google picks it up and we've got a link from the google.com domain?