I've been spending some thought on the Ancients the last days and think that's a good area to do some work. It's more conceptional and does not require working out anything specific at this point.
To refresh this subjects, I think the best way to deal with supernatural beings is to treat spirits, ancients, and demons as basically the same thing. Life force taken form and creating consciousness. Demons are the standard type that inhabite the universial Void in which all the universes of the Material Planes exist as bubbles of matter and laws of nature. When the Material Planes first start to form they are very similar to the raw Void and demons can pass in and out of them, but as the differences increase, the borders between the world become (almost) impassable. The beings formed from the life eneries of the new Material Planes are the Ancients, who are different from demons, but still share some similarities. As the Material Planes continue to change, so do the energy beings which eventualy became the spirits. But deep below the ground conditions have barely changed at all and the spirits of these regions are still very much like they had been aeons ago. Some of the most powerful even managed to continually persist through the aeons, hence all the spirits from deep below the ground are called the Ancients.
(A special case are the deities of the Earth and Darkness, which have changed into spirits but originally had the nature of Ancients, which very few people know about.)
Maybe the most important or at least prominent of the lesser Ancients are aboleths. Also there are theit scum servants, which they create by mutating captured people from the surface world.
Doppelgangers would fit great, but it begs the question why they look humanoid and have the ability to mimic humanoids when there are almost no humanoid creatures inhabiting the underworld. But then, having an illogical creature that makes only sense in regard of the surface world might not neccessarily be a bad thing for aberrations.
(Or as Keith Baker reportedly mentioned in regard to Eberron, it's not the question of why daelkyr look like humans, but why humans look like daelkyr.)
I also like the unfortunately underrepresented Phasms. Shapeshifting slime is awesome.
I like umber hulks, but I don't really know what to make of them other than large wildlife. But you do need those as well, same goes for carrion crawlers.
Also the Underworld needs gibbering mouthers. Because, let's face it, they are shoggoths.
Derro also should be right at home in the Underworld. Cannibalistic albinos and so completely insane it's even one of their special powers. Whether or not they are native or mutated gnomes probably just get left open and unanswered. I am not completely sure about grimlocks, though. They would make decent enslaved humans that were left wandering the Underworld, but I'd rather like to limit the number of humanoid races to a reasonable number and there's already so many of them all over the place.
Also worth mentioning are goblins and fish people, whether you call them Deep Ones, Murlocs, or whatever you like. They are very old humanoid races and the only surface creatures that have any experience with traveling to the Underworld. However, they are still natives of the surface world and part of "normal" nature.
Going into more obscure creatures, I also have Tsochars in my sight. They are a race of sentient eels if you will, which connect together to form a shared neural network that is capable of conscience as a single mind. They then crawl into bodies of larger creatures and take them over. Since they are already considerably big, it can get a bit like the alien roach in Man in Black wearing the Edgar suit.
For the Great Old Ones I already have a few candidates in my sight. The main concept is something similar to the Daedric Princes from The Elder Scrolls and Eberrons Cults of the Dragon Below, or the Twilight Hammer Cult from Warcraft. Not completely evil, notout to destroy the world, but even more alien than spirits in general. And unlike demons, they are part of the world. However, they are much more rarely encounterted or even heard of by people from the surface world and only worshiped by small, isolated, and extremely weird cults.
I want Tiamat, the ancient divine five headed dragon. It's a leftover from very early first drafts, but I love that deity and even though dragons themselves are not Ancients and I don't plan on Tiamat to be the creator of dragons, I just think she would fit in well. Or at least I want to get her to fit.
There also happen to be five types of dragon in the Barbarian Lands, just of slightly different color.
Also Dagon. In D&D he's a demon, in Lovecrafts world he's a giant alien thingy. I think there's a good place for a giant ancient fish-squid thingy inhabiting the deepest oceans of the spiritworld.
And lastly Tharidzun. There's nothing generic about him and it will be a straight ripoff with just a different name. But he's the coolest god from Greyhawk and I think he's great and would just fit very well.
That's what I have in mind right now and toying with. Some thoughts and ideas from you are as always appreciated.