I think that the most effective bosses are the ones that are truly terrifying. In
TP we've got a spider (which is just plain scary in the first place) so massive that you need to control giant statues to beat it. In
OoT, we have Bongo Bongo. At first glance, just a pair of hands! How freaky is that? And then, the rest of him is invisible, but his eye is where hsi neck is. That truly scared me when I was a child. In MM, we have to fight a mask with tentacles. Okay, those kinds of things, to me, make the most effective bosses. So, instead of being physically horrifying, cause that is just so outdated, how about we make it mentally horrifying.
Here's an idea I've been tossing around for a while that I think would be good. Let's say that you're walking through a temple. You hear something approaching, turn around, and there's the boss! A giant, grotesque troll in armor. You run forward to battle it, but what's this? You haven't gotten the item that can beat him yet! What will you do? Run away! So, you run away, and the first thing you're thinking is, "Man, this is no ordinary dungeon, there's not even a boss room." So, you spend the entire dungeon being constantly afraid of this thing popping up around every corner.
So, after fighting your way through the dungeon, you finally get the Big Key, you find the door and put it in. In it is a chest. This has got to be the item you need. But just as you walk up to it, the boss comes flying down from the ceiling and steals it. Now what? Well, you couldn't beat it without an item before, but this room is different. There are spikes all over the walls. So, you use an existing item in the first phase of the boss to ram his hand into the spikes and force him to drop the chest. Once you do that, you grab it while he is stunned. You reach into the item chest, but it's empty. There's nothing in there! So, what you have to do is eventually use the items already at your disposal to lock the boss in the chest.