ER is an unusual show by modern standards. Before season 4, there were maybe 3 or 4 episodes that even used incidental music. None used pop music except in context of bars, karaoke, or the radio. In many ways, this let the actors be actors and kept the writers on their toes; no bad dialogue could be hidden from the audience with surging strings or adult contemporary fluff.
Even in Season 4, sonic manipulation was still used sparingly. You get the jarring and wonderful use of "Crucify," by Tori Amos, played at a girly sleepover at Elizabeth Corday's. Watching this now, that says more about the presence of Tori Amos in pop culture back then, which directly opposes the current perception of Amos as a producer of "gothy lesbian" music (which I never bought, but it was the general barrier to entry of other people I know). "Good Riddance (Time of Your Life)" by Green Day was repeatedly sung by Scott Anspaugh and Jeanie Boulet in scenes that were absolutely heartbreaking. It's good to know that there was a time BEFORE that song, and Green Day themselves, became synonymous with cheap sentiment.
So in Season 6, when music began to be used in earnest you end up with the most sublime use of pop music and the most irritating, within 2 episodes of each other.
HONORABLE MENTION
"Bookends" by Simon and Garfunkel. Used twice for scenes of Mark Greene and his dying father, you can see an entire history in Anthony Edwards' eyes, of memories that he missed out on, that he could never experience again.
BLAH BLAH LA LA ADULT CONTEMPORARY
What should have been a beautiful scene was ruined by Don Henley's "Taking You Home" (who, frankly, has ruined many more tv shows, songs, and bands than can be documented. Perhaps a post for our sister blog The Oncoming Hope: Music). The long awaited (and final) reunion of Carol Hathaway and Doug Ross, was already sentimental enough (in a very very good way). So when the producers decided to overlay drippy acoustic guitars and Don Henley's warble, it took me so far out of the moment that I had trouble enjoying the scene.
THE PERFECTLY SUBLIME
I may be biased because this is one of my favorite songs of all time period, but it just captured (and foreshadowed) the state of John Carter's life, long after his brutal stabbing and the loss of star pupil Lucy Knight. It played at the beginning of the final episode of season 6, which went in directions no one could ever have predicted. Of course, once all is revealed, it becomes perfectly obvious. But the song comes in just to give a little bud of the truth, and then a series of unhappy coincidences brutally opened that bud to both the viewer and to Carter's colleagues.