Here are some other tunes that stuck with me (all of the scenes contain spoilers, but the songs are just songs):
"Light and Day" by The Polyphonic Spree / Scrubs Scene
"Heard Ya Talkin'" by Jeremy Kay / Scrubs Scene
"Fighting for My Love" by Nil Lara / Scrubs Scene
"Sinnerman (Felix da Housecat Remix)" by Nina Simone / Scrubs Scene
"Book of Love" by Peter Gabriel / MASSIVEST SPOILER WARNING Scrubs Scene
"Fresh Feeling" by Eels / Scrubs Scene
"Over Me" by Tricky / Scrubs Scene
"Good Time" by Leroy / Scrubs Scene
"In The Sun" by Joseph Arthur / Scrubs Scene
Here's a list suggested by others in this thread:
"Sideways" by Citizen Cope / Scrubs Scene
"More Than a Feeling" by Boston / Scrubs Scene
"Respect" by Erasure / Scrubs Scene
"99 Luftballons" by Nena / Scrubs Scene
"Hey Ya (cover)" by The Blanks (a.k.a. Ted's Band) / Scrubs Scene
"Koyaanisqatsi" by Phillip Glass / Scrubs Scene