I think they're very organized, but then again, I mostly just use that site for books. The manga is organized alphabetically in letter sections and when you click on a title, there are also links to all other books in that series, dvds, music, toys, and other merchandise from the series. Also, if you mouse over a link, it'll show a picture of what the merchandise looks like, so you don't have to go through the link first to see it. I think it's utterly fantastic.
Most manga books are around $2 cheaper there. If they're over $10, Amazon sometimes has a better price, though. In that case, it's good to check both places.