The Great Deku Tree.

 

Can't believe no one else has brought this up, the first iconic death:

Bambi's mom.

 

Jason Todd's death in the Batman comics.

 

In before ned stark and dumbledore mentions... oh damn.

In HP, there's a lot. Cedric dying was a huuuuge oh fuck moment. Then Sirius. Then Dumbledore. Then Snape.

I third Ben Sullivan's death. I've seen the episode probably over 10 times, and it's still a sad moment.

Shephard Book and Wash as well. I knew that happened before I actually watched the show though, but it's not the knowledge that it's happen, it's the when.

Deckard Cain's death in D3... though more for the fact that WTF were blizzard thinking, having the most iconic character get killed by Rita Repulsa.

Barrin from MTG, obliterating a phyrexian horde at the cost of his own life. And urza later on, and gerrard

just off the topof my head

 

Most of the ones I'd pick have been said already, so I'll just pick my favourite deaths from the lot.

Mistborn - Kelsier, Elend and Vin.
Lord of the Ring - Gandalf and Boromir.
Dresden Files - Shiro, Aurora and Morgan.
Harry Potter - Harry Potter and Dumbledore.
FMA - Maes Hughes.
Doctor Who - 10th Doctor.
Firefly - Wash & Sheppard Book.
Watchmen - Rorschach.
Tengan Toppa Gurren Lagann - Kamina.
Code Geass - Lelouch.
Cowboy Bebop - Spike Spiegel.

 

Sean Bean in... Wait, fuck.

Xena at the end of the series

Wesley in Angel

Bobby Singer in Supernatural. Also Gabriel.

Jonathan Kent in Smallville

Rachel from Animorphs

 

I'll second Rachel from Animorphs. Shit hit me hard, man.

Couple that stood out to me:

The dog in I am Legend. Movie was just meh, but damn if I didn't choke up a bit when the dog kicked it.

Creasy's death at the end of Man on Fire.

 

Definitely this. Loved that movie.

Also, Tess Mercer in Smallville and John Winchester in Supernatural.

 

Only death I can think of that wasn't mentioned here was Rita in Dexter. The kid, the blood, the bath tub, and Dexter, still showing no clear emotion.

 

How has nobody mentioned Obi-Wan and Yoda? Add Darth Vader for that matter.

EDIT: Also, I submit the deaths of Lee Scoresby and Stanislaus Grumman from HDM, not to mention Coulter and Asriel.

 

Darth Vader in Star Wars.

The deaths in Malazan,

Eidt: Ninja'd >_>

 

Tara dying was probably the death that hit me hardest in the long term. However, I think Buffy's death in season 5 was even more sad. Particularly with Giles murdering that guy just to make sure Buffy wouldn't have to do it.

Oooh and in season 1, too. "Giles, I'm sixteen years old. I don't want to die."

The Green Mile was really sad, too.

 

Everyone in Goodbyeee, Blackadder 4.

It was the first time we studied WW2 in High School, and she showed us each episode, followed up by some written work. It was the first thing I remember where the main characters all died.

Roy Batty, Rachel, Rita and Mufasa have already been said.

 

Dude, spoilers!
I suppose in this kind of thread it is to be be expected.

Off the top of my head, I'll have to say Whitebeard from One Piece.

 

The Hobbit was first published in 1937. The statute of limitations on spoilers has expired long ago.

 

Trying to avoid those that have already been said.

Ellie, from Up. To be fair, it's just one part of that whole sequence, but damn if it doesn't get me every single time I see it.

Moridin, in Mass Effect 3. Same for Thane. Two of the best characters, and some of the best writing in the entire series.

Beak, in The Bonehunters (Malazan series). A character you think is just a nutjob suddenly pulls off one of the most badass feats of magic in the entire series, sacrificing his life to save an entire army. It's astonishing.

A couple of ones that I've just encountered, having finally finished Dollhouse; Bennett and Ballard. Not because I necessarily cared about or even particularly liked them, but they were just such shocking, sudden deaths. Also Topher.

Ganner Ryhsode from the Star Wars EU - you've got to love a guy who takes the last stand to such epic proportions that the enemies he's fighting start worshipping him as a god.

Fred Burkle in Angel. The most brutal death Whedon ever wrote (seriously, he destroyed her fucking soul!)

(Also in full agreement with the shouts on Blackadder, Joyce Summers, Roy Batty, Wash and Shepherd Book, Lee Scoresby, and Ben Sullivan)

 

Ash in the first Pokemon movie, even though it wasn't actually a death. That whole movie was pretty powerful, considering its target audience, and that scene in particular.

Mami Tomoe losing her head and Madoka dying repeatedly. Followed closely by her apotheosis.

Mrs. Landingham and the fallout in the Washington Cathedral.

Darth Sidious, as his death marked the biggest victory for the rebellion. And that wrinkly bastard went down swinging.

 

It's like being kicked in the crotch over and over again. I can still remember the dull sense of horror when I first saw Mami die.

This is the only death scene that can consistently get me to cry. It's freaking heartbreaking.

 

I second Lee Scorseby, Coulter and Asriel and would like to add Will's father to the list. Would've been the perfect book ending if Pullman hadn't one upped himself in the next page.

Lelouch. Best ending evah.

 

Lavitz Slambert - Legend of Dragoon. This has to be my first main character death as a child
When I first played this game I had no idea my favorite character was going to go like that. It was even more heartbreaking when I met him again later in the game. All I could think of was what Dartz would say to Lavtiz' mother.

Zack Fair - Final Fantasy 7/Crisis Core. There's just something about taking on an army by yourself to save your friend and then dying afterwards. What made it really bad was playing his final few minutes and then the cutscene afterward.

Spartan B-312 - Halo. Pretty much the same reason Zack Fair's death stuck with me. Staying behind on a dying planet to help give others time to escape, then having to fight enemy after enemy until it's just too much. The cracks appearing along the visor as you took more and more damage really made it great, along with seeing the fallen Spartans along the level.

Maes Hughes - Fullmetal Alchemist. This death got to me because I wasn't expecting it at all. I thought Maes would come through alright, and it was even more tragic that his wife's form ended his life. The bit with his daughter afterward was heartbreaking.

Nicholas D. Wolfwood - Trigun. Oh man, I saw the anime before I read the manga. There are so many parts of Wolfwood's death that just stuck with me through the years. From the blood trail he leaves after talking to Vash, to his "I'm not ready yet! I don't want to die!" line and everything afterward. The Manga death also stuck with me when I later read it. I thought the final toast between him and Vash was amazing.

Portgas D. Ace - One Piece. It was mostly what he said after he took the hit that got me. I love things like this. Sad deaths are my favorite kind because they just become so memorable.

JoJo's Bizzare Adventure - Pretty much every fucking death in this is fucking sad. Stop hurting my heart Araki you damn vampire.

Charlie Gordon - Flowers of Algernon. Reading the reports as he regressed just destroyed me. I could not for the life of me stop crying as I finished the book.