timppu: Can you give some examples? I'm mainly aware of CD-ROM talkie versions, but are you referring to possibly different versions across different platforms? Are they cases where the talkie version is not the best one?
Then again, doesn't GOG still miss many alternate versions for some Sierra adventure games? Like the VGA remake of Space Quest, which to me is quite a big omission.
Well for example there are 3 DOS versions of the Secret of Monkey Island (that I know of), none of them talkie. There was a 16 colour EGA floppy version, which is as far as I know the original. There's the 256-colour VGA version with redone backgrounds (no sunset =( ). Then there's the CD version of the 256 colour version with redbook audio, a different interface and a missing joke.
I don't think it's possible for one of those to be considered objectively "the best" version. They all have unique good points and bad points and that's not even counting the SE with it's voice acting (yay) and "upgraded" graphics (boo!). There are of course versions for other platforms as well, the Amiga version having unique versions of the music but only 64 colour graphics (which I think are downgraded from the VGA version rather than upgraded from the EGA).
There are even more convoluted situations with games like Loom, but I know more about Monkey Island.