I would not put a javascript main feature on the first page. Anyone browsing with a noscript add in immediately has to either allow the site or sees nothing but the side menus, and it appears more like an add than your main content. It should at least have an alternate display. It also has an odd gap even after you tun the javascript on, since it does not take as much room as your left menu.
The category product listings are crowded. The thumbnails being on a separate row would separate them better, and some of the info can be on the individual product page instead (SKU, for example, really isn't part of a summary to get someone to look at the item, and the add item section is rather wide for a table like that with the arrows, some of the descriptions are long for that sort of list). I think the price is normally on the right, next to the add item section in web stores... it's odd to look for it in the middle.
Featured products should be at the top. It's not much of a 'feature' if you've already seen all the products by the time you see that section. Perhaps that could also be on the main page to fill in the gap under your other content.
The twitter, facebook and youtube links are not very obvious with that sort of picture, and I'd expect to find those and some of the other info in one of your top menu links... (free shipping perhaps could be more an about us & policies? Or maybe you could put those links in with contact us?).
Overall, it's quite usable and clean and has no major problems. I would stay away from so much javascript where it is unnecessary - your cart already appears to not need it, and that is where it may have been more useful. It is not needed for an FAQ or to shrink your front page into what looks like an ad. I would normally browse a site like that with it turned off, as it seems to not be completely necessary to make a security exception, and then it doesn't look as you would like it to for your customers. When it adds significant function, then it's great, but it's not something I'd rely on for basic content display.