Callie Tyrol (Battlestar Galactica)
There is a lot of death is Battlestar Galactica's final season, but Callie Tyrol's funeral was the most heartwrenching. Regardless of your feelings about Callie, seeing the Colonial Fleet grieve for one of their own was heartbreaking, and made even more gut-punching by Laura Roslin's presence. Dying of cancer, she says to Admiral Adama that she likes the service, and wants him to know what she likes.
Carson Beckett (Stargate: Atlantis)
You can file Carson's death under one we didn't see coming. After removing an exploding tumor and delivering it to an awaiting guard, the tumor exploded anyway, and the blast killed him. After three years, Carson Beckett was considered the heart of Atlantis, and watching his send-off back to earth was a particularly hard moment for fans of the show. Watching him being eulogized by Dr. Elizabeth Weir, and his casket carried through the gate by the rest of his friends was devastating. The show never seemed to be the same.
The Eleventh Doctor (Doctor Who)
It's timey-wimey, but the Eleventh Doctor's death in Doctor Who Season 6 Episode 1, "The Impossible Astronaut," still had viewers sobbing. After The Doctor was shot at Lake Silencio, River, Rory, and Amy gave him a Viking funeral because a Time Lord's body was too precious to be left lying around.
Amanda Clarke (Revenge)
Amanda Clarke's funeral was a sad one for sure, but it was also wrapped in duplicity. The story of Jack Porter and Amanda Clarke was one of childhood romance, but the Amanda Clarke he married was really an imposter. While he's heartbroken to lose Amanda after finally being reunited with her, it's also sad for Emily Thorne (aka: the real Amanda Clarke) who thought of her former juvie cellmate as a sister.
Prue Halliwell (Charmed)
The oldest Halliwell sister, Prue Halliwell died off screen after the Charmed Season 3 finale. Season 4 opened with Piper and Phoebe mourning their loss and wondering how they'd continue to be witches after The Power of Three had been broken. The show was able to continue by introducing a fourth half-sister, Paige, but the first act of the Season 4 premiere is full of grief and sadness for the sister they lost.
Quentin Coldwater (The Magicians)
Quentin Coldwater's death was a loss for The Magicians and the memorial in which the cast says goodbye is particularly saddening. It wasn't just that Quentin was getting ready to move on and observing the proceedings, but also the way his friends chose to honor him. Between the mementos being thrown into the fire and the cast singing an emotion version of A-ha's "Take On Me," it's hard to keep a dry eye.