A good nominee would be Conan The Barbarian. There really is no perfect version, but some might prefer the DVDs because of their cuts.
The first DVD: 1982 theatrical cut. But very poor picture quality, no extras, bad print.
The second DVD: A new directors cut, with better picture and audio, and tons of extras. But no theatrical version and picture quality still leaves some to be desired.
Blu-ray: A third version, which incorporates a few bits from the old directors cut. Extras are pretty good, but the picture quality is not the best example of Blu-ray technology.
The Blu-ray is my preferred version because of the picture quality but it's the cut I like the least. I'm still not sure why they took out the best scene from the DVD directors cut (Conan and Sabotoi making sticks on the beach) but left the boring ending which kills the crescendo. For this reason I sometimes wish I could watch the theatrical cut, but the quality of that first DVD is pretty bad.
Was hoping the Blu-ray could finally have both versions and make everyone happy but instead it made things even more complicated.