Some changed that instantly jump out that I remember (using a scrubs wiki for track names etc). Don't know what they've changed them too just that they aren't any songs I've heard before.
http://scrubs.wikia.com/wiki/List_of_music_featured_in_Scrubs (I think the are the original/DVD songs and the are Netflix/rerun changes though not all changes are listed)
"My Big Brother"
"Something's Always Wrong" Toad The Wet Sprocket (End of the first episode with Dan)
My First Step:
"Bad Case of Loving You (Doctor, Doctor)" Robert Palmer (when the pharmaceutical rep is introduced)
"My Fruit Cups"
"Ride Wit Me" Nelly (end of episode where Eliot gets cut off from her Fathers money and they drink champagne at a fancy place)
"My Monster"
"Dreaming of You" The Coral (When JD and Eliot get together at the end which leads to them being Sex Buddies (da da da daaah) )
Some are the same like the use of Under Pressure when Elliot is packing up her things from her apartment. It's such a shame because I think Scrubs has some of the best licensed music choices out of any TV show. Just glad I have the full 8 seasons on DVD.