The final ship in FTL habitually murders me, especially the advanced version - including when I'm flying around in a ship that can beat the snot out of basically everything else. It's never been anything other than nasty even when I won.
If you count optional bosses there's also Nightmare King Grimm (the dream nail version, not the normal version) which makes The Radiance look like a sluggish chump. Then there's the postgame really optional bosses, which just get out of hand, leading to yet another version of The Radiance which is far nastier.