Thanks John. This was a big help. Looks like the concept of semantic markup hasn't really resonated with e-commerce developers. Most of the markup in these apps is *far* from perfect. BTW, I found a contender not in that thread called SelectaCart.
I've played around with Zencart a little bit just because Dreamhost has it as a one click install option (so I can't speak to the manual install process). It is a little time consuming to customize, but it was decent. The code behind isn't perfect, but it is pretty good with respect to having "decent semantic markup", comparably.
I did a site with SquirrelCart a few months ago. It is not standards based by default, but if you want to take the time, you can modify the tmpl and css files...