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SEO Programs

There is no software for manual SEO because if you use a software as a strategy in SEO it means you are using an automated techniques. I've been using Article Marketing Robot for article submission, Wiki bot for wiki submission and SB bomber for social bookmarking. I can say that these tools are very effective to increase traffic and back links.
For the low paying clients, I use IBP and ultimate demon for link building, at a slow pace.

I would strongly recommend you watch what your doing with those program though, as you could very easily over-do the link building to low quality generic websites and recieve a penalty, you could also unsuspectingly link into a bad neighborhood.

For clients that are paying more I prefer everything done manually, each with their own campaign goals. For analysis I use ahrefs.com / seomoz`s open site explorer / google analytics / WMT and experience.
I am agree with Sitebee. You should be careful while using automated software or I suggest you not to participate in such activities. I haven't seen any genuine firm using automated software for promotion because It may ban your website too.