I am fortunate in that I have yet to notice. (I used to have a player that had a little idiot light that would light up whenever the disk was set with this on -- it never went on, as far as I noticed.) I suspect in my case it's because I listened to very little classical and/or jazz at the time. Actually, now that I think about it, I listen to more than I used to, it might be more of a problem now.
I agree with Reks -- the best way to listen to them is to play them in a player that handles pre-emphasis correctly.
What does EAC do? What does iTunes do? Hmmm...must investigate. I suspect it'll be like HDCD -- there's really nothing like the real thing. I'm sure there's a way to do it in software, and I wouldn't have a problem with it, except like HDCD, it'll probably be kludgy unless it's built in. (I know of no way to do with iTunes; and even with EAC, one has to manually decide when to turn it on or off, and I'm still not sure it'll be doing it right.)