One of Ash's main pokemon in D/P is a emotionally scarred and has flashbacks, I thought that was pretty dark.
Also I saw the episode where James gives up his Cacnea just yesterday. Goddamn man, all of these feels. Most often when someone releases or trades or gives away a pokemon it's for the good of both of them, like a natural part of life or something - Ash's butterfree had to go because it was in love, Ash's Pidgeot had to go because it had a duty to protect its kin.
James, though, had to give up one of his close friends because he realized the hard way that he was not a good enough trainer and that, no matter how hard he tried, he would never be a good enough trainer, and that his own incorrigible incompetence makes him have to give up his Pokémon.
Pokémon is harsh, man.