Watchmen was a good example of this, though it might make sense to own both movies.
The BR release was the extended cut. The UE BR version had Tales Of The Black Freighter woven into the storyline. Some people complained about adding 30+ minutes to the length of a 3 hour movie, and some people not familiar with the comic wouldn't know what to do with them.
LOTR of course is the prime example of this waiting for the "later" version.
QoS might get a double-dip, though Casino Royale's double dip was vaguely worth it. As my non CE verson of CR was a freebie from a B2G2 sale, I didn't mind double-dipping.
Cars' double dip, which was just an audio upgrade, not really worth it.
Some movies, I don't mind the occasional double-dip, as long as I'm not out that much money for the "first" release.
Monsters vs. Aliens might be one that double-dips, and that would be to add the 3D version to it. May not happen, though you never know.