Hey Alec! For a boss you should make a demented/twisted/evil version of ECCO the dolphin (of course it can be a generic dolphin) But that would be funny to see since it reminds alot of people of ECCO 
It would be a pretty cool hidden easter egg. You break a wall, and a dolphin swims free singing some tune from Ecco.
But i think that Ecco is under the protection of copyright laws, so it might be a pain to get a permission to use it.
If you're going to add hiden things, make a remake of a fish or something from the SNES's "Evo: Search for eden"
You could probably get it from a couple of sites, just to map out the dude. I found out about the game in the 50th issue of Nintendo power. It's one OLD issue, man. It has Kaepora Gaebora, that owl, on the cover.
I'm really against adding all those Easter eggs. As much as we all can't help but think of all those great games which Aquaria reminds us of, Aquaria is its very own game. Whether or not there are obvious similarities, I want Aquaria to do its own
thing. This game should keep any straight references from other games to a minimum or to nothing at all. Aquaria is, from what I can tell, tiring to be one of those games with a deeply impressive story and I don't want to have to any thing that would break this pattern and say all the sudden "Look, you found Ecco".
However, this is simply my opinion and if anyone here has played Eternal Daughter and found the secret room you'd know that there where a few, "in you face" references to Metroid, Cammy and something else I think. So I think there is more of a chance you'll see something like that in Aquaria, rather than not.
Other than that, I'd love to see game related hidden eggs.
