I should add:
PHP code (or other scripting languages) should have every file, function, and method commented as well as blocks of code and complex conditionals...
CSS should be self commenting (i.e. good class names) Although I like to separate out blocks of CSS with comments so it makes it a bit easier to find the "area" you're looking for. I generally separate out the CSS classes by what page they are used on with general (site wide) classes having their own group.
I don't comment queries unless they are very complex... they should be self explanatory.
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