You could try using the DNG converter to see if they will convert to DNG and then see if they can be opened in Camera Raw. If that doesn't work then you'll probably have to open them with ViewNX and create TIF copies. Those should open in Camera Raw. Not the best solution, but if you don't have the original files still on the card there isn't much else you can do.
DNG didn't work either. I also used ViewNX to convert NEF to TIF but as you wrote this is not the best solution. However, I could see the pictures at least...
But! I've just found a nice solution and I can now recommend it for everyone who will face the same stupid problem: http://owl.phy.queensu.ca/~phil/exiftool/fix_corrupted_nef.html
Here you can find a software to fix Nikon Transfer's corruption, it worked to me, and this is great!
Have you done a byte-wise comparison of the corrupted files against non-corrupted? Perhaps there is some easy fix if one is armed with the aforementioned info. - dunno...
If you post a pair I'll have a look.
Uh, they are 42,3 MB each...
Most people post links to files uploaded via yousendit.com or the like. - but at this point: no sense re-inventing the wheel (you've got the solution already).