I jus listebed to a really interesting piece from NPR's All Songs Cnsidered about this, an interview with someone involved in the profuction.
listen here
He starts with a discussion of what remastering is, what source material they used, and the things they decided to "fix" without ruining the integrity of the recordings. He played a shirt clip to demonstrate how they took an obvious recording error (backing vocal track dropping out for a moment) and fixed it the way the Beatles certainly would have if they had the capability. To be honest I listened 3 times and couldn really make out the difference. Such audio quality things are clearly lost on my ears.
More interesting to me was the discussion of the difference between the mono and stereo mixes. He focused on Sgt. Peppers which probably represents the biggest difference between the 2 sibce the Beatles themselves oversaw the mono mix while they left the stereo mix entirely to George Martin. The guy in the interview made a case for the mono mix being his preferred, and I'll say he was pretty persuasive. At the very least it certainly justifies the existence of both box sets from a completeness standpoint.
Well worth the 20 minute or so listen.