I know this one gets brought up a lot, it is a great episode, but my My Lunch/My Fallen Idol is my favorite followed shortly by My No Good Reason/My Long Goodbye are my favorites. They pull at my heart so much for different reasons.

But yes after that My Screw Up ranks with it and pulls at me too

I think scrubs is one of the best shows ever, I have not come across another show that blends comedy with serious drama and characters who grow like scrubs. The way it can be silly, then dead serious and it doesnt feel forced or uneven, it just works