Now, I'm going to admit that I Live in England, so I can't comment on the many versions available to other countries. So, to begin:
1988 - the first video version is available. It runs for 105 minutes. It is missing the 20th Century Fox fanfare at the start, but what the heck, it's Batman.
1995 - the fi;m gets a re-release, but there've been a few changes. It runs for 100 minutes, it has the fanfare at the start, and a trailer! Also, it's been digitally restored so that it is even more colourful than the 1988 version!
Now, I used my BATCOMPARITOR INDEX
(Okay, I ran both films and timed them) and the 100 minute version is the same as the 105 minute version, so maybe they've sped it up slightly. But you wouldn't know otherwise. However,,, 
There IS a difference other than the above. When Batman is on the phone to Admiral Fangschleiser, he whistles a song as he's searching his rolodex. in one version, it's Anchors Away, but in the other, it's What Shall We Do With A Drunken Sailor!
When the Batmovie came to DVD in 2001. the 1995 version seems to have been used, and another change is evident, to wit, the film is now widescreen, and it looks as if that has been achieved by cropping the image to achieve the desired result. When the film was released on Blu-Ray it seems to be the same print, more or less.
So, at least THREE different versions of the movie. Which is the right version?