The most noticeable difference in behavior I've seen in the VGA CD version compared to the VGA floppy version is that some text was (accidentally?) cut in the scene where you bribe the Monkey Island cannibals.
There are some graphical differences besides the user interface, though. Mostly it's subtle differences in colour. I suspect some of them may have been caused by the colours being ordered differently in the palette. At least with things like the smoke from the voodoo lady's cauldron. That change carried over to the special edition, too. Maybe it also explains why the actors are a bit brighter in the CD version? Unless that was a deliberate change.
(I had to use a demo for the EGA version, since I don't own a copy of that game. Hence the difference in text.)
But the most noticeable colour difference, and one that I'm sorely tempted to fix in ScummVM because I think the CD version is harder to read, is the sign about the dogs:
One other graphical difference was probably introduced by mistake: When playing the floppy version from hard disk (rather than directly from the floppies), the close-up of captain Smirk has animated cigar smoke. The same smoke animation as for the cauldron, apparently. I'm guessing whoever updated the game just mechanically removed those checks, and only kept the case without the smoke.
Restoring the animation in ScummVM turned out to be easy, but getting it to appear a the correct position and with the correct colours took a bit more fiddling:
The only case I've seen where graphics have been redrawn, rather than re-coloured, is the meat in the SCUMM Bar kitchen. The floppy version looks like ribs to me, while the CD version looks like a leg. And while preparing this screenshot, I just noticed that the colour of the grog changed to green.
Edit: This change may have been to match the animation when you use the hunk of meat later?