This technically isn't a Pokémon "owned" by Ash, but I think Ash's goodbye with that wild Butterfree during Decolora Adventure was the saddest for me. I found it really heart-wrenching for a couple of reasons: firstly, he reminisced about parting ways with his old Butterfree, which made him feel a strange sense of nostalgia that we typically don't see in Ash.
Furthermore, BW Ash actually cried... and I mean BW Ash. By this point in time, Ash has already parted ways with sooooo many other friends, companions, and Pokémon in the past, to the point where he's actually used to it. That being said, seeing him cry like that felt like a very special occasion for BW, especially when we consider that he was almost essentially reliving those same sad moments all over again.