The main ones I've had that I can remember are from the Dragonball franchise.
In Dragonball Z, two times. Once when Goku sacrifies himself to send Cell to King Kai's planet to prevent the villain from blowing up the Earth, and again with Vegeta's death during the Majin Buu saga, after having a touching moment with his son and sacrificing himself to destroy Buu.
And I cried at the end of Dragonball GT. Yes, even I want to treat GT as non-canon to the Dragonball franchise, but the end of GT just made me feel like the series was finally at an end. With Goku going to Shenron to the Dragon world, as he says his goodbyes to everyone.