404 page needs meta description (just to make Google happier)?

The most important thing for your 404 pages is the header's status code: it must be 404 not found.

It's maybe stupid to say that, but in dynamics applications, with an URI like this http://my.webapp.invalid/index.php?id=4, when id=4 return nothing, many web developers returns a 404 message with a 200 OK status code...

An other thing: for example, if someone try http://my.webapp.invalid/index.php?id=toto whereas id only accept integer, it's not a 404, but a 400 Bad Request that you must return.

It's easy to handle this, for example, with the header function in PHP or the HttpWebResponse.StatusCode Property in .Net

No. Why worry about your PR for your 404 page. I would be more worried on making sure none of your links end up there in the first place.