Jurassic Bark would be on my list too.
The episode of Scrubs "My Screwup" when Dr Cox's friend Ben, (Brendan Fraser,) dies due to leukemia complications, (it was in remission,) and the fact that he's dead is revealed at the end showing that Dr. Cox has been in denial the whole time, only accepting it when arriving at Ben's funeral. They play "Winter" by Joshua Radin too. Holy Hell, it made me sad that Brendan Fraser was dead, that's a massive accomplishment right there.
On second watching there are all these visual cues that Ben's dead, (despite the fact he keeps turning up for the rest of the episode,) but I didn't actually click until the funeral as I imagine most others did. It was masterfully done.
Then they play the banjo-happy Scrubs theme right afterwards, it's like "What the Hell are you doing? Dr. Cox is sad!"
Some Simpsons episodes tear me up, the first and last ones with Homers Mum were tear-jerkers.
And yeah, another million points from me Tankichi - Clone High is awesome.