Ojamajo Doremi Naisho, in episode 12 near the end when Non-chan's mother comes to see Doremi, she tells her that "she couldn't make it". Cue one of the biggest Tear Jerkers of the series.
In a late episode of X/1999, Karen and Yuto kill each other, while Satsuki struggles with the Beast and is eventually killed by it, too. As Yuto lies dying by the fountain, he remembers making a promise with Satsuki earlier and says with a faint smile: "It seems tonight, I won't make it for tea..."
In Fullmetal Alchemist when Hughes dies, he apologizes to his family for not being able to make it home.
I got a 404 Error :/ Apparently the page didn't make it.
The Two Towers movie has a strange example because that scene was filmed before the script was totally ironed out, the director wasn't sure what actually did happen to Aragorn, so decided to keep the dialogue vague to save time:
Used interestingly in The Fifth Element: towards the end, when they're in the temple, David says quietly to himself "We're not gonna make it" and sighs, unwittingly activating the 'air' stone (by breathing on it), which leads to their figuring out how to work the rest of the stones and saving the world.
In the novel Jurassic Park, Grant asks about the ultimate fate of Ian Malcolm, who was badly injured when the T-Rex escaped. The character being asked only shakes his head. He got better and showed up in a later novel, stating that rumors of his demise were grossly exaggerated.
The standard line is used in the sequel, The Lost World, after the antagonists' attempt to steal a T-Rex egg goes very badly for one of the trio:
On Arrested Development, George Sr.'s doctor tells the family that he's "gone" and that "he just got away from us". It turns out that he meant George just escaped through the window. It became a running joke how the family is never sure how to interpret anything the doctor says.
Home Improvement: When Tim told Jill about her father's heart attack.
Also on Will and Grace, when Will tells Grace about his father's heart attack after his mother calls.
Rucks of Bastion delivers a long string of them; as the Kid wanders through a village, Rucks gives the name of every ashen corpse they walk by, before adding "...didn't make it".
In the first Mass Effect, one of your party members does the nonverbal version after the Final Boss(before Shepard emerges unharmed).
In Halo: Reach this is how Noble 6 tells Kat about Jorge's death.
In Sonic Adventure 2, right after the end of the True Final Boss, Sonic returns to the space station alone, where everyone else was waiting. Rogue notices this and hesitantly asks, "Shadow...?". Sonic just shakes his head and brings Shadow's bracelet to Rogue to tell her what happened.
In World in Conflict, a private gets sniped in a cutscene. Directly after the scene, this phrase is used about him.
Disney's Hercules. Herc sees Megara lying there, and doesn't ask. But Phil looks up at him sadly and shakes his head anyway to confirm his fears.
Pixar's Cars T oons, in the Mater the Greater episode of the series, at the end Mater is relating the Jump over Radiator Springs gorge, which was made by Lightning Mc Queen, and then they cut back to them, when Mc Queen asked what happen he gets a "You didn't make it" and then Mater goes out, followed by the two forklifts from his story who sadly look at Mc Queen as well.
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Not, in this exact wording, what Mario said to Luigi about the origin of his football.
