I'll start off with the most unintentionally
hilarious death instead, that being
Ernst from Ys: The Ark of Napishtim. It's probably the only instance I can remember where a boss attempts to assume a more powerful form and just winds up disintegrating himself (and you didn't say it had to be protagonists.

).
Best is a pretty hard choice, but these days I'd be a bit of a minority report and actually go with
Eldeel From Ys: Mask of the Sun. The genuinely tragic antagonist is a really,
really hard thing to pull off, and the game managed to nail it pretty hard- one of the things that the game does put a good chunk of effort into showing is that
Eldeel really was, and perhaps, still is a good man, but that the temptation of reviving the ancient power and prestige of his fallen race, and the chance to elevate himself from prisoner to god-king was just too much to resist. The two most important aspects of theatrical tragedy is that the fall is able to seem both simultaneously avoidable and inevitable, and include the element when the tragic figure recognizes he has done wrong, and this is one of the few instances where it actually comes off.
Worst death, however? Well, there's a whole lot to choose from there, unfortunately. I would have to go with a fair chunk of Knights in the Knightmare, because at some point it just gets repetitive. yes, we get that your setting is a horrible cesspool of misery and death. Dear lord, the Dept. Heaven setting is one of the few places I know of where things were drastically
improved by the apocalypse.