While I don't have any specific ideas, all I know is that currently bosses are incredibly generic and that some intensity would be awesome. Most bosses also seem to have the 'I am big so I'm important' attitude. Sometimes the smaller faster bosses can be the ones you remember. Though I'm not saying we have to do anything quite as intense as Iji's menagerie of alien superbosses, but there are some good ideas for 2d sidescroller bosses there, and the same goes for Terraria, Megaman and Castlevania for interesting mechanics. Probably cave story too. (I haven't played it yet) Also, Boss dungeons, that way you could have environments tailored to certain bosses, and that would be awesome.
I'd like to add two things. First. Given the levels of equipment available during the boss battles, I'd say that the penguin boss is easily the most difficult one. This I feel is because it can crash through blocks... it's far too easy to kill the other bosses given that they can be trapped inside of them, locked out of a safe area, and attack between with ranged weapons. Only the Penguins felt like a real boss battle to me, because it had a special ability that no other creature in the game has besides the player. The other bosses just seem like bigger aliens with more health. Second. I like your avatar.
I remember The Legion from Castlevania. It was a big boss, but it didn't move. I thought it would be easy, until I hit it. The way it spawned dead bodies and the whole fact that it was a gross floating mass of dead bodies gave me chills. Perhaps Starbound can make some scary bosses too.
