Depending on how much free time you have and how broadly you want your Web site to be "advertised" through search engines, free submission might be a very reasonable alternative to paying submission services to do this for you. I recommend expensive programs only to big Web sites that have the necessity (and capital!) to get their site out there in every possible way.
What's also a problem is that many submission programs submit to search engines and directories you have probably not ever heard of. Really, how many search engines do you use on a regular basis? Probably only one or two. Remember, you have to focus on the masses. Advertisement through search engines is extremely useful, but is pointless when the search engine you submit to is rarely used by anyone. (You can probably do some market research on what "audience" uses which search engines most frequently or which are the most popular ones.)
Free submission services can be very useful, but watch out for spam email and "free offer" boxes that are clicked when you submit! Also be sure to read the terms and conditions on these sites. I once submitted a site and found my inbox filled with more than 25 (!!) emails from "partners" of the submission program.
If you have some extra time, the best thing to do might be to just visit the search engines yourself and look for their (sometimes very well hidden!) submission pages, and just input all the information manually. This might take you awhile to do. What I used to do is make one "template" in a text document in which I typed my site info, keywords, description, etc. and then just copyied-pasted it to each of the submission pages of the most popular search engines. This may take you awhile, but it will save you money.
Good luck with submitting your site, and be sure to choose carefully from these options in site submission. Read the specific information on the submission site before jumping to conclusionsyou might just find some surprises (pleasant or unpleasant) on their terms and conditions and program description pages.