If you run an ecommerce site proper SEO is even more important than if you run a content site. Why you ask? Well you see ecommerce sites generally have lower traffic and higher income per visitor than a content site. What this means is that even a small increase in traffic can create a large increase in revenue. It is thus very cost effective for an ecommerce site to expend money on search engine optimization.
For the most part an ecommerce site can optimize the same way as a content site, what with adding keywords and all of that. However there are some issues that, while they can exist on a content site, almost always exist on an ecommerce site. These issues are outlined below:
It is extremely imperative that you setup your ecommerce site to use search engine-friendly URLs and if you can help it, meaningful identifiers. Most ecommerce sites are database driven and by default most shopping carts are not search engine friendly. This presents a very large problem because search engine may have trouble navigating to your product pages. Letting a search engine index your home page is not enough because people often search for exact products. For instance if you ran a golf store you would find that while some people do search for "golf clubs" they usually search for a specific brand or model club. To give you a more personal example, last year I saw a vase I wanted to buy for my mother in one of those generic "Gift" catalogues. I thought I might be able to find a better deal online though and so I searched for the 5 word product title on Google. I found a site that had both better deals and search engine-friendly URLs and I bought the product there.
There are three ways you can handle this situation. One way is to detect search engines by accessing the HTTP_USER_AGENT variable and to turn tracking off for them. This is technically cloaking, however it is benign as you're using it to show the search engines what your visitors can see. Of course malicious cloaking is showing search engines something your visitors do not see.