http://www.ecommerce-blog.org/ http://www.varien.com/blog/ http://www.thinkvitamin.com/features/design/webtogs-diary-of... http://www.seomoz.org/blog/17-new-rules-for-successful-ecomm...
There are a lot of turn-key solutions, like Yahoo or Ebay Stores, Amazon's Webstore, and a few more. Others let you build their code into your site, which can make for a more seamless appearance, but also involves a lot more coding work. Really, your product might dictate your software, so maybe you should figure it out first, and then concentrate on which features you want. They usually all have tradeoffs and benefits. Like I said, its hard to get good, objective info on them, but figure out your business first and then start looking.
How would you analyze the transaction/inventory/shipping process of woot.com?
How many things will you be selling? Also important, do you make it yourself or does someone else make it and you'll be reselling? There are a lot of options for selling on commission (aka Amazon), dropshipping, and the like.
How do they get these items? How do they manage their vendor/supplier relationships?
They probably use drop-shipping since they are only selling one product at a time.
Now, where they get them is a mystery. They could have connections to close-outs and liquidators or distributors that could get these items in bulk.
For some software ideas, you might actually want to check out this: http://news.ycombinator.com/item?id=232958