Gamer's Charmander, who was turned into one by 'M following torture.
Pink the Audino, who was blackmailed by 'M and turned into part glitch. Several of the other characters even stopped what they were doing just to give her a hug.
Each of the trainers have had their moments of woobieness, with special mention probably going to Anom (especially during the Oblivia and the Alternate Timeline arcs) and DS (again, especially during the Alternate Timeline arc).
Doc, Tagg's Audino, who's mother was killed in front of him and who also got turned into a Shadow Pokemon.
Tracer's Salamence, Nadia, who not only had to deal with Tracer missing her evolution but also getting temporarily grounded after Tagg's Hydreigon broke her wing.
Riku, Lyuri's Sandslash, being responsible for the death of Lyuri's parents when he was just a baby and suffering a lot of guilt because of that. And also for being constantly bullied by one of his teammates. And even then he was involved in an accident that got his best friend, Zap, hospitalized, fortunately, things seem to be getting better for him.
Edward the Dratini, his first appearance has him getting beaten up by his first trainer and the scene where he fought Goldie was heart wrenching.
Orre managed to turn a few characters into this, notably Sakura, Lyuri, Herbert, Eskay, Duke, and Crewe due to the suffering they had to endure at the hands of Cipher.
Shaka - Constantin's Gallade, -has had quite the depressing life. Watching his trainer get abused as a child, one of his close friends killed, having his sister released, his trainer snapping and going off the deep end and having to perform the will of his trainer regardless of his opinion due to The Vow. It's hard not to feel pity for the guy.