In this recent post to his blog Anthony Ferrara looks at commenting in your application's code and how to be effective (and not so effective) when using them.

A few weeks ago I was sparked into a twitter conversation with Larry Garfield (@Crell) about the value of comments in code. [...] A pretty innocuous comment [about code that doesn't have comments] that is quite insightful. [...] That led to an interesting discussion that just couldn't fit on twitter. So let me explain...

He defines what he means by "comments" (DocBlock, general comments and legal information) and what sort of things should be inside of them. He also points out a few things not to do in you comments including being overly descriptive and restating what the code is doing (they should be less about that and more about the "Why"). Of course, there's exceptions and he touches on those briefly to finish out the post.