I have a lot but if I chose a "minor" one, it'd be Mochizuki from Tsukikage no Kusari: Sakuran Paranoia. If I remember correctly, it's more of a "merry bad ending" rather than a completely tragic one.
Mochizuki's insecurities, emotional dependence, and attachment become much stronger. While the heroine and Mochizuki may still end up together, their relationship develops in an unhealthy and isolated way. Instead of moving toward a positive future, they become trapped in their own small world.
What makes this ending memorable is that it feels both romantic and unsettling at the same time. It was a very "Mochizuki-like" ending because it takes the themes of his route like loneliness, dependence, and longing. Pushes them to the extreme. Also, the voice actor (Yoshitsugu Matsuoka)! I love the way he calls her name so dearly every time.