(forked from bug 593624 comment #2) Not sure why the list of the 'Most Visited' default smart bookmark and the list found by clicking the dropmarker of the location bar do not match, since they seem to serve the same purpose, as far as I can tell. We should make them both display the same list. Pick the more useful one, of course. I'm using the 'General' component (instead of 'Location Bar' or 'Bookmarks & History'), since I'm not sure which list's algorithm is better. If these lists really should be different, by all means, enlighten me. ;)
I suspect it's frecency vs. frequency plus some adaptive learning, but can't find evidence of that by digging around Bugzilla. I did find bug 426864, which is a pretty important difference. It also doesn't make much sense to me to have two primary UI elements that duplicate the exact same thing (although I suppose the Most Visited list is on the no-longer default toolbar now).
also bug 424454 explains some of this. Markdak could easily explain what is going on here though.