Software that optimizes your website for you is not recommended. If you want software for keyword research & such, that’s a different story.
Different search engines have different criteria for high-ranking websites. I’ll just assume that you want to rank better in Google cuz they’re the biggest.
Google’s big thing is inbound links. Quantity doesn’t matter nearly as much as relevance and quality. Focus on getting one-way links from websites related to yours (topically) and who are in good standing with Google.
I believe that reciprocal links and a spurt of low-quality/questionable quality links still work for Yahoo. I don’t know about longevity with this method, but it worked for me for several years.
MSN seems to pay attention to you after you get some low-quality links from spam-like sites (or submitting your sites RSS feeds), but MSN focuses more attention to your website’s content than the value of inbound links.
However, since there’s a large overlap here on what works & what doesn’t for certain search engines - I would checkout sites like http://seobook.com and some webmaster forums like webmasterworld.com, forums.digitalpoint.com and so forth & listen in on some of the SEO conversations over there.