The Blu-ray contains the 2006 "Remastered" version and the original versions. I actually interviewed the producer a couple weeks ago:ray_afraid said:
I grew up hating Star Trek. All I knew of it was The Motion Picture, which is one of the most boring films I've ever seen, and The Next Generation, which is full of pseudo-drama, techno-babble and very dull and dry characters. But, for whatever reason, I've been watching the original series on Netflix... And I love it!
However, I'm guessing someone has pulled a George Lucas on it as many shots of the Enterprise look very CGI. Am I wrong? Some shots really stand out as being 'new'. I like this stuff enough to invest in some DVDs or BDs, but I wanna see it the way it was originally broadcast. Is that available?
http://trek.fm/standard-orbit/standard-orbit-6-a-little-bit-of-icing.html
They were careful to not mess with the edits any, no Greedo shooting first or anything. I go back and forth on which version I prefer, but having the original effects goes a long way towards my acceptance of the new ones.