@quiet_samurai: right on about the intro tutorial... but as some other people have commented, that can prove to bore me right out of the game. And I'm not sure it can encompass all that a user manual can offer.
@Mythomaniac: great thoughts about the intro being repetitive. (yes, I see the irony of pointing out that being repetitive is boring, and that I just repeated the comment

)
@cyrad: To your example, Portal proves that if done correctly, it's not so intrusive and actually fun as hell.
I am a technical writer and to hear you all agree that a user manual isn't so bad encourages the heart! Whenever I describe what I do it usually begins with: "You know those manuals you never read... I write those."
And I also agree that it shouldn't just be restrained to 4 languages telling you press A to shoot. Some back story is always awesome, and even gets your brain into the imagination part of the game play as well.
I would also not be completely turned off by offering it as a PDF online in order to save a few trees. (I'm not completely evil.) I would want the option to print it out on my own though.