As far as I've found, its only a function of individual apps. Goodreader is an example, it allows you to lock orientation either way.
I agree it would be a great feature and supprised and disappointed it was not done in iOS5.
A jailbreak app called SBRotator allows you to do this... although I believe it's a paid app, not for sure. Of course would require you to jailbreak your phone and such.