One of the most important aspects of an effective SEO strategy is the ability to research, analyze, and ultimately select the keywords that are most likely to result in success for your clients. There are a variety of free tools available on the web specifically designed to help online marketers do just this. Each tool has its own unique methodology for collecting and presenting this data. Comparing any of the tools’ results without knowing the subtle differences can lead to incorrect inferences and an SEO strategy based on misinformation.
The primary difference is that Long Tail Pro is a big time saver over MS. With Long Tail Pro you are able to enter in multiple seed keywords at once (rather than just 1 with MS). So, instead of entering in 1 seed keyword, waiting five minutes, then going back and entering in one more; you can enter 5 seed keywords (for example), hit generate and then see all the keyword ideas at once!
The Search Based Keyword Tool is intended for researching keywords within Google’s Adwords network. Unlike the Keyword Tool, the Search based Keyword Tool is based solely on searches from Google.com. This factor causes the search volumes displayed to be considerably lower than the Keyword Tool. Because this tool is intended for paid search keyword research, it contains additional information on Suggested Bid and Ad/Search Share. The Search Based Keyword Tool is seamlessly integrated into the Google Adwords interface and allows marketers to add keywords to their PPC campaigns without having to login to their Adwords Client Center.
The limit on manual keywords could be higher.  I personally wish we could input 10,000 keywords at a time, instead of 200.  However, I understand the costs that Long Tail Pro has to maintain each time a new manual keyword is input.  Not a deal breaker, I just wish the limit was higher. (To be fair, I don't think most keyword tools have a bulk manual option at all).
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