Sonic games aren't exactly known for having hard bosses, but for me, it has to be the final boss in Sonic Superstars against Fang as Trip. It's the hardest boss simply because of how long and painful it is to defeat.
To add to the frustration of this game's infamous bosses, this one takes the cake.
It's long, tedious, has moves that can insta-kill you, and takes forever to cycle through attacks. On top of that, if you die (which is very likely), you have to start all over from the beginning. I hate this boss so much.