This special edition DVD gives you the choice to watch with deleted scenes inserted into the movie, which I did.
There's a new scene when they're in Area 51. It was right before the Fresh Prince brought that live alien in. Data was in the crashed ship showing Dr. Ian Malcolm around the technology... "we know what this does *oops broke it off*... but we don't have any idea what this crap is..." refering to the Matrix-looking code on a monitor in the dashboard. Jeff Goldblum says, "Oh yeah, look at my laptop.... that's their communication code that I've been deciphering," and you can see the same matrix-looking code on his laptop, at which time Data says, "You know, you're starting to make us look bad."
I just found that scene to be significant because it supports the "use the Apple laptop to upload the virus into the alien mainframe." It suggests that maybe he was actually speaking the aliens' language (at least their computer language), which makes it slightly more plausible.