The Chronicles of Narnia: The Lion, the Witch, and the Wardrobe - doesn't include the extended cut on the Blu-ray and drops a DVD full of extras.
King Kong (2005) - would've been great if they compiled the hours and hours of bonus features onto a BD. As is, you need to keep 6 or 7 DVDs of extra features!
Spider-Man 1 & 2 - the first releases were barebones and they still didn't bother to include all of the extras when they re-released them
Pearl Harbor - the BD is missing the Director's Cut, commentaries, and 2 DVDs of extras
A Clockwork Orange - they apparently remastered the film for its 40th anniversary but used the older master for their Anniversary Edition BD.