Does Amazon not run their website on AWS? I assumed (incorrectly, apparently) that AWS was originally built to allow Amazon to scale their own services. Is it really a separate product that they don't use themselves?

Just because the servers themselves are up doesn't mean that the software running on the servers is up (or that it's capable of handling the load).

I just got my shopping cart to load, but it took quite a long time. Maybe they're getting DOSed.

Just because Amazon is down, doesn't mean the infrastructure is the reason. They did build AWS out of the technology they used to build Amazon, but its unclear if they are using it directly or use an isolated set of services.

Amazon uses AWS to host Amazon.com (retail), although you can imagine that they dodge the billing structure and have quite a number of resources dedicated away from the main AWS fleets.

Originally, that's true, Amazon didn't run on AWS afaik. But i believe they do now.

Nevertheless, they still have application architecture which sits above the aws substrate. It's perfectly feasible for them to have seriously fucked up a deployment that runs on top of AWS, which may be functioning just fine (and at least all of my services running out of us-east seem to be up and running).

Just because a site is on AWS does not mean it cannot go down for its own reasons. There are more failures possible than infrastructure.

I thought the same. Werner Vogels, their CTO, said at the NYC cloud event that they moved amazon.com to it in 2010, and amazon.com international in 2011.

Incorrect, Amazon.com runs on AWS: https://news.ycombinator.com/item?id=5588012

AWS tech maybe, but you can be pretty assured that the data centers (or at least networks) are are almost completely segregated.

Nope, its all mixed outside of software segregation.