Ok, I will start off with my #1:
Saving Private Ryan- where one of the Americans gets killed in the house to house fighting, on the second floor of a house, by a german with a knife in a slow agonizing wrestling match which ends with the american soldier slowly getting impailed with a trench knife by the german. Man. 
So lets hear some of yours.
(SPOILERS, obviously)
Tad’s death in Cujo.
Elf-yes, that stuck with me too. Then I saw a Friends episode where the guy who got killed is a real A-hole. I figure, hey, he deserved it! 
This might be incredibly LAME but the death that struck me the most was the death of Raistlin in Time of the Twins (I think that was it). It struck me for more than one reason actually. The reason that won’t ruin the book is that I am, actually, a identical twin-as was he.
I cried when Optimus Prime was killed. Bastard Megatron!
Optimus Prime died?
Damn you Mendoza!
The death of the young boy at the beginning of Clive Barker’s short story, “Rawhead Rex.” Especially the line, “He was sick down its throat as it bit the top of his head off.” That is so frigging visceral.
In Stephen King’s crapfest Rose Madder, the crazed male villain goes looking for his wife at a shelter for battered women, and in the process casually murders one of the women there. It just struck me as unnecessarily brutal and random, and unlike King.
I have absolutely no idea what the story was called, but in 3rd grade our teacher read us a story over the course of several weeks (a chapter every other day or some such) about two friends and their adventures. Towards the end one of the boys is killed when he is stung by a swarm of bees (he’s allergic). To this day I can hear Mrs. Wheeler reading that story and how sad it made the entire class.
The death of the replicant played by Rutger Hauer in Bladerunner. He didn’t so much die as simply stopped, a life unfulfilled.
The murder toward the end of Heavenly Creatures. It’s a good film and I’ve watched it several times, but I can’t stand to watch that scene. Brutal.
The death of Boromir as he defended his friends in the Lord of the Rings.
Especially his dying words to Aragorn. It just was filled with so much honor, tribute, and friendship that I was overcome.
Also The Iron Giant sacrifice and his final words.
Garp and Owen Meany from their respective John Irving novels.
In Freshman Eng 101 I read the short story “How to Tell a True War Story.” As this came out of the Norton Anthology, I’m sure I’m not the only one to have encountered this peach of a tale.
Though I’m a bit sketchy on the details (a case of wilful repression), a good portion of the story dealt with the torture, killing, and eventual stuffing-down-the-well of a baby elephant (or was it a bison? maybe a dog?) Thinking back on it, this was probably meant to be great symbolism mixed with subversive political undertones, but shit if I care! As far as I’m concerned, that was nothing more than the literary equivalent of a snuff film.
It’s been awhile since I read it, so I may be off on a few details.
There’s a chapter in Stephen King’s “The Stand” that discusses people that survived the super flu, but died as a result of the collapse of society. Among them were a newborn that starved to death in the maternity ward, a junkie that ODs from uncut heroin, and a devout Christian that wants to take his life after he loses his family but won’t. He jogs most of the time to distract himself, and during one of his runs he has a heart attack and thanks God for taking him just before he dies.
::plnnr if you care, sure sounds like that was Taste of Blackberries::
Little Women, for sure.
I cried when Tracy died in On Her Majesty’s Secret Service. I was reading the book. Called a friend for sympathy, he’d read it too. None was forthcoming. Evil bastard. Probably shouldn’t have married him.
Anna Karenina’s suicide. I can still recall how horrified and frustrated I felt at the time; if only she could have managed to get up!
The rat in Ben
The dog in Old Yeller
The mother bear in The Bear
Bambi’s mother in Bambi
Simba’s father in The Lion King
Come to think of it, there hasn’t been one human death in any movie that has moved me to tears. Damn, I am one messed up dude.
I too have never gotten past the death of bambi’s mother.
Spock’s death in Star Trek II, The Wrath of Khan. That and the subsequent funeral are one of the very few times a film brought me to tears.
Kirk: Of all the souls I’ve encountered in my travels, his was the mos…<he chokes back the tears>…human. <queue bagpipe music playing amazing grace>
The endings of Pandora’s Box, Ashes and Diamonds, McCabe & Mrs. Miller and Dead Man.
I’d agree with Rutger’s death in Blade Runner. Just an awesome overall scene, and he gives one of my favorite movie quotes:
“And all of those memories, lost in time like tears in the rain.”
Nothing incredible simply reading it, but when you see it in the film, it’s great.