MEGA MAN X1
This enemy can jump, but for whatever reason this never actually happens in-game. The code for it still exists in the game though, and can be easily triggered. He will jump a short distance (32 pixels?) towards X, then when X is in range, fire his mace-ball thing.
Here is a youtube video of this behavior in action.
Lost Zero charging palette?
Zero has two palettes in the ROM that aren't used in-game at all. Presumably they are for some kind of charging effect. In the final game, his head crystal glows to indicate charging.
What it might have looked like.
The third Anglerge
There is both data and a palette for a third kind of Anglerge boss in the game. The subID for this Anglerge is 129, while the subIDs for the two Anglerges in the final game are 128 and 130. This Anglerge only blows air at X. Since the first Anglerge sucks air in, and the second Anglerge both sucks air in and blows air out, this was probably meant to go in between the two.
No idea where this was supposed to go, and the graphics won't load up correctly. This object is closed at first. When it opens up, it fires out two Tombots in one direction (which direction depends on the subID), then closes again. X can only damage the object when it is open. When it is destroyed, it starts smoking from the bottom for a bit, then stops.
Flying drill enemy
Probably the most interesting find. I hope I can find the graphics to this thing, it has a really cool looking animation cycle. This enemy doesn't appear at all in the game, and its behavior is completely unique. It has the same ID as the Sine Faller enemy, but has a subID of 1. The enemy falls down from the ceiling and swoops back and forth. When it collides with the ground, it drills into it, leaving only a small part of its sprite visible above ground. It only takes 1 hit to kill.
That's it for now. I'm bound to find more stuff as I keep delving deeper into the ROM.