This has been discussed pretty much to death, so you'll be able to find a good number of threads on the subject, if you're interested. But just to sum things up:
Paramount titles are pretty much identical across both formats, I think. But for Warner titles, check the audio specs and extras list of each release. A lot of the time, the HD-DVD release is the one to go with for two reasons. Up until this point in time, Warner has not ported over the TrueHD track from their HD-DVD release to their BD release. So with the BD release you get no lossless track, with of course gives the HD-DVD release a major leg up. It looks like this will change in the future, as the back of the box of The Departed BD release shows it has a PCM track.
The other advantage some Warner HD-DVD releases have over their BD counterparts is the titles which have an IME track, or Picture in Picture commentary track. These have not been ported over to their BD releases, because of the mess that is BD-J, so that is more added value with the HD-DVD version over the BD version of some movies.
Of course, some people will be quick to say that is the HD-DVD version is a combo disk, it's a disadvantage for that format's version, because it adds a few bucks to the cost. But it's pretty clear that for a lot of titles, the HD-DVD release with a TrueHD track and IME hold the advantage.