And their estrangement since filming the movie.
I’ve never seen it, but I’ve read that there was some irony or poignancy or something similar reflected in Henry and Jane Fonda’s onscreen father-daughter relationship in On Golden Pond.
Robert Downey, Jr., doing an amazing impression of an out-of-control cocaine addict in Less Than Zero.
Similarly, but even more on this point, is this Ryan Adams video, which was filmed 9/7/01 and prominently features the WTC. Not really an “offscreen” reason, but very poignant.
Led Zeppelin in 1973, the year the WTC was completed: “I think this is a song of hope.”
All of The Crow.
Weird…I was coming in to say Heath Ledger in TDK, too.
But it was the tunnel chase scene that did it for me…in a split second, my thoughts went from “this is incredible!” to “…oh. And this is the only time I’m ever going to get to see him doing this, isn’t it?” 
“Under the Boardwalk.” Not a scene, but a song:
[QUOTE=Under the Boardwalk]
The song was set to be recorded on May 21, 1964, but the band’s lead singer, Rudy Lewis, unexpectedly died of a suspected heroin overdose the night before. Lewis had sung lead on most of their hits since the 1960 departure of Ben E. King, including “Up on the Roof”. Rather than reschedule the studio session to find a new frontman, former Drifters lead vocalist Johnny Moore was brought back to perform lead vocals for the recording.
[/quote]
The song is supposed to be about horny teenagers. Instead it was about pain and loss and why a friend was gone. The pain is palpable as the singers try to work through their grief while propping up a, “The show must go on,” attitude.
Maybe the saddest pop song ever.
Cordelia mourning Doyle’s death in Angel Season 1, watching his video.
“Is that it? Am I done now?”
In real life, the actor who played Doyle died a few years after.
Similarly, Lorne’s last scene in the final Angel episode, walking away in despair/disgust after killing Lindsey, saying they’ll never see him again. Andy Hallett died four years later
THIS, THIS, THIS! A thousand times THIS! No matter how many times I’ve watched this montage before the end credits, I still tear up. And the Elton John tune “The Last Song” is just as fitting and tearjeaking.
The night he died, I went out with Mr. Rilch-to-be, came home and watched Dogfight. I wasn’t sure which scene would be the one to make me break down. It was the one where Rose/Lili Taylor plays and sings the Joan Baez song.
Just a little boy standing in the rain
The gentle rain that falls for years
And the grass is gone, the boy disappears
And rain keeps falling like helpless tears
And what have they done to the rain
And Eddie/River sits smoking and watching her intently. My eyes are stinging a bit now, in fact.
[tangent]And 1993 was the same year DiCaprio first started getting noticed, with Gilbert Grape and This Boy’s Life. He stepped into Phoenix’s spot so neatly, it’s VVC.
Kind of like John Candy –> Chris Farley –> Jack Black
River Phoenix in My Own Private Idaho, as I think it reflects the troubled life River led when he was younger, (Children of God Sect etc..) I was a big fan of River as a teenager this particular film seems to touch me more than others. His last words in the final scene:
I’m a connoisseur of roads. I’ve been tasting roads my whole life. This road will never end. It probably goes all around the world." 
Hearing Amy Winehouse’s “Rehab” was already hard to listen to without having a heavy heart before Saturday’s sad news.
Or in “F-me pumps:”
Don’t be mad at me
‘Cause you’re pushin’ thirty
And your old tricks no longer work . . .
Needless to say, she herself never came close to pushing 30.
Also really sad to see how healthy she looked way back when.
…this scene from the TV Series: Avatar:
In itself, the scene was very sad. But then we find out the segment was dedicated to Mako, the voice actor for Uncle Iroh in the same scene, the result is devastating. I still cry every time I watch this.
“Leaves from the vine
Falling so slow
Like fragile, tiny shells
Drifting in the foam
Little soldier boy
Come marching home
Brave soldier boy
Comes marching home”
In* The World Is Not Enough*, Desmond Llewelyn, who played Q in 17 James Bond movies, introduced John Cleese as his replacement, and when Bond asks him a question he doesn’t want to answer, he says: “That’s one thing I learned from you Bond - always have an exit strategy.” and uses a platform in the floor to vanish from sight.
It was his last on-screen performance and he died a month after the movies’ premiere.
The Phil Hartman/Jan Hooks “Love is a Dream” sketch from SNL. Without Phil’s death, it’s just a weird bit of odd left field sentimentality from a show not known for it… but it turned out to be Phil’s perfect “obit clip” when SNL returned from hiatus after his murder.
Okay, now speaking of Jack Black, the scene in Tropic Thunder where his character “confesses” his addiction, still thinking he’s got everyone fooled, is a bit uncomfortable, being as Robert Downey Jr. is in that scene.
In season 5 of Dexter there’s a scene between Dexter and his sister saying how much they mean to each other. Watching it is kind of surreal knowing about Hall and Carpenter’s off-screen relationship, his battle with cancer with her by his side, and their eventual break-up.