The only directory that matters right now is DMOZ. You can submit to that one by hand. Getting into the Yahoo directory costs an amazing $300/year/site, and IMHO is not worth it because Yahoo defaults to Google searches anyway.
Altavista & Inktomi are the only two search engines that matter after Google. Both of these have a paid inclusion that you can do by hand; I'm not sure how effective these search engines are, but I would recommend them if you are looking for the maximum amount of traffic.
Overture and Looksmart are two PPC (pay-per-click) search engines. However, there is no automatic submission process to get into a PPC engine because you have to bid on a keyword. If you are willing to pay at least $0.05 per unique visitor, then Overture and other PPCs are definitely worth looking at.
The so-called FFA pages are completely worthless. You might be in 1 million of these, but you won't get a single hit from any of them. In fact, it could hurt you... Google may penalize you for being in too many FFA pages.
In short, stay away from any automatic submission service... they are all worthless!
Try asking some questions at this forum:
searchengineforums.com
Good luck,
David