I just did some work for a client who has a large ecommerce website. We moved to Volusion, which was their decision, but I have to say I was very happy and impressed with
SEO features, flexibility offered with the volusion package. Things like friendly URL's, keyword rich titles for each product page etc made deep op much easier than the "other" shopping cart softwares Ive seen.
For Keyword we use Keyword Discovery and WebCEO pro. Keyword analysis is only as good as the brain behind it. While quality data is key, insight into the site niche, analysis of of web stats and analystics are important as well in gathering a strong and balanced (its not all KEI) keyword strategy.
Have fun above all else!
John