I prefer to do SEO manually, because it is much more relialbe. SEO tools can be mistaken in some cases and can make problems with the correct optimization of your site.
Depends what you want to do! Do you want keyword research and SEO competition analysis? Then Market Samurai. I could list plenty of other great software for other needs. PM me if you want me to send you some links.
As far as helping me with SEO (submissions, posts, etc.) I use SENuke. I also like Scrapebox for comment postings. For SEO competitor info, I use Market Samurai.
As stated before, it really depends on what you are trying to achieve. I personally prefer getting in there and doing it myself... then just cutting and pasting the waffles on my mirrors if needed. I been using SEOQuake toolbar... to check ranks... its a bit overwhelming at first.. but overall its good.
Software Tools Paid Market Samurai, Micro Niche Finder Free tools that help with various aspects of research and SEO Google Keyword Tool, SEOQuake, SEO Spyglass, Google Wonder Wheel, Google Insights Paid services that help with backlinks Unique Article Wizard, Social Media Science also referred to as Synnd Paid software that helps with social bookmarking Bookmarking Demon, SocialBot For link research and finding links Scrapebox For stand alone automated software submission to various types of sites ArticleBot, RSSBot There are various aspects of SEO on page and off if you include back links and various ways of marketing so I had to list what I consider all the best software.
Most of SEO software, even the best ones such as IBP, Web CEO are not for helping your site ranked first page instantly as you may expected. Those softwares can help you with tedious work such as backlink checker, ranking checker and find potential links for your site. However, most of SEO which could help your site really is manual done by youself only.