Lots of whitespace improves readability, as does the use of a sans serif font. Deviate from either and a lot of people will hit the back button because they can't easily read your text.
A clear call to action massively improves conversion. The rectangular button in a dominant colour will increase signups by 10-20%.
960px wide because the majority of web users can see a page this wide without scrolling. For the same reason, all the important stuff on the site should fit within the first 500px vertically. a 960px grid is highly divisible and so gives you very flexible layout options with minimal hassle. There's a strong argument for 720px, but it's largely a question of browser demographics.
The links in the footer should be stuff for people who know what they're looking for, providing greater information density without added clutter. It works in large part because it's a convention, but it works nonetheless.
Familiarity matters in web design - the better people can predict where things will be, the better they can navigate.
That isn't to say that all these websites work as well as they should do, but there's only one reason to deviate from the norm - if you've tested something and found that it converts better.