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I have recently tried ripping some blu-ray discs (Rear Window, Indian Jones) and the resulting files have been closely cropped on the sides - almost like a pan/scan process. Well, under the circumstances I am losing a significant part of the frame. What am I missing here?

You mean like this?

http://www.blu-ray.com/movies/Rear-Window-Blu-ray/7738/

Don't know about Indiana Jones, but sure looks normal for Rear Windows. The film isn't 16:9 to begin with.

I've noticed it most during the credits... not all of the names fit into the frame. For "Raiders..." it was even more pronounced..