Greg Linden links to a heavily lesson ladened LISA 2007 paper titled On Designing and Deploying Internet-Scale Services by James Hamilton of the Windows Live Services Platform group. I know people crave nitty-gritty details, but this isn't a how to configure a web server article. It hitches you to a rocket and zooms you up to 50,000 feet so you can take a look at best web operations practices from a broad, yet practical perspective. The author and his team of contributors obviously have a lot of in the trenches experience. Many non-obvious topics are covered. And there's a lot to learn from.
The paper has too many details to cover here, but the big sections are:
In the recommendations we see some of our old favorites: