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Tear Jerker: Mai-HiME
The ending theme.
Episode 5 has Mai's flashbacks to her mother, and her realization that choosing to ignore the Orphan bus led to deaths and memory erasures.
Mai-HiME episode 8, when Akane watches her boyfriend Kazuya get killed and is rendered functionally comatose for a good portion of the series, episode 20, when everyone starts fighting each other and poor Takumi becomes the next casualty, evaporating in Mai's arms after Akira's CHILD is struck down (even Mikoto broke down into tears when she realizes it was her fault), and episodes 24 and 25, where Yuuichi dies in a way that seems so coldly logical when you see it and still manages to die with a smile on his lips, and where Natsuki and Shizuru kill each other in an inevitable double-KO both saw coming. At least one of those will get tears from you, though with the first two, the sheer awesomeness of the twist might leave you too stunned.
Even if Akane losing Kazuya leaves you too stunned for tears (and it did for me), the following events are utterly heart-wrenching: No-one knows what happened, they think Akane and Kazuya just eloped, and the high school comedy continues as normal. Then, when we finally see what happened to Akane after that scene....
Talking of Takumi, how about the scene shortly before where he decides he won't go to America for a possibly life-changing but very expensive operation because he knows how much of a burden he is to his sister — unaware that she's listening? This troper, who knows what it's like to care for a sick relative, cried so much that when it came to the actual death scene he had no tears left.
Nao's definitive defeat at the hands of Shizuru is even more tear-jerking. Specially when Nao has an Heroic BSOD, starts crying and screaming for her Missing Mom, who spent several years comatose and was killed when Shizuru killed her CHILD.
This troper did not have much sympathy or respect for Nao through the series, but seeing her like that, not just defeated, but completely broken, kind of changed his view point in this moment that felt like an intense, odd combination of both tearjerker and heartwarming.
Don't tell me you forgot Haruka's death and the flashback to her and Yukino's childhood?
The ending of episode 15 might count, too, after Alyssa is shot to death and passes away in Miyu's arms, and then Miyu takes her corpse and seals herself in a lake in despair. The choice of ending music for this episode doesn't help at all.
Let's talk about episode 23, with a defeated Midori staring into the distance after basically sacrificing the man she adores to preserve what might or might not be a chance for someone else to live. "I'm sorry, Professor, but you would be proud... right?"
Takumi's apparent death in the manga, particularly his sister Mai's reaction. He gets better... but then things get much worse.
The part late in Episode 25 when Mai reads all the names of the people who lost their loved ones in the conflict, a list that includes some of her friends. And then Shizuru and Natsuki are added to that list.
The final episode jerks tears of the happy variety, as everyone lost is resurrected.