Comment on WordPress SEO Tutorial by SEO Dave.
I use WP Super Cache because it’s the first WordPress caching plugin I tired (never tried W3 Total Cache) and WP Super Cache plugin is working well on my sites.
I’ll have to find the time to test WP Super Cache vs W3 Total Cache since if there’s a big difference it means your sites run faster if you use the right one.
I can say if you are torn between the two and currently not running caching plugins on your sites pick one of them and see how it goes because what is certain, whether WP Super Cache or W3 Total Cache you should be using caching plugins because they do have SEO value.
Update: Feb 2014 have since tried W3 Total Cache and it’s a better caching plugin SEO wise. The SEO value today (2014) is even more important with Google taking page speed (how fast a site loads) into account in it’s search engine algorithm.