I started out using software like MNF and MS but as time goes on and I get busier I have found that just using the Google keyword tool is fastest and easiest, and most accurate. MNF and MS take forever to load all the results. The bottom line is that if you are good at analyzing your competition and know search handles that MNF and MS use it is just as fast and accurate to do everything manually IMO. This is how I do my KW research now:
Google keyword tool using exact search
Pick out the top phrases I want to analyze
Do a search with the following handle: intitle:"kw"inurl:"KW"inanchor:"KW"
Once I do that I run an SEO analysis with Traffic Travis to see how optimized in terms of KW in title, total backlinks, PR, Yahoo directory, DMOZ, domain age, etc I am up against for top 10.
I think people overanalyze way too much! Now that I have many sites ranking in the top 5 I laugh at all the overanalyzation and analysis paralysis that goes on in this and other IM forums. The bottom line is this stuff is actually pretty easy if you just put it to use. It's not rocket science and everything you need and WAAAAYYYYY more is on this site.
A good domain, optimized title, optimized content, an seo optimized WP theme, and a strong VARIABLE link building campaign is all you need to make it to the top in most niches. Then the question is, can you do anything with the traffic? Can you make the sales? Can you handle the phone calls? Does your sales funnel work?