I haven't seen any of the nominated films for those categories this year (well, In Bruges and WALL-E are up for best writing (original)), so I can't compare. Really, it comes down to taste. Films like The Dark Knight aren't as popular with the oscar voters as with the public. The voting systems are a little ecclectic too, so it could have been on many voters' shortlists without actually making the cut.
I guess you could argue for its nomination in any of those categories: directing in particular - I think Nolan will get one eventually.
Ultimately, the Oscars aren't that big a deal. Lots of good films have been overlooked over the years.
I've seen it argued elsewhere that WALL-E should be up for best film.
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