So, I think Monica and Frostfyre are on to something, but here's some ideas straight from my head to the paper to here:
So this is a rough concept of an icon I came up with. In the center it's half a brain and a protractor, to represent how the topics here are a cross between science and imagination. Then the orbiting bodies are, well, orbiting bodies, moons of some sort, to give a somewhat more concrete implication that the circular object in the center is meant to be interpreted as a planet, and also to suggest that we deal with building worlds of all sizes. In the top right I've drawn a tiny version, to show that it works pretty well when that small (though I still don't know how to draw a brain).
So this would go on the top, you know, with the site name and all the buttons. There's a lot going on, so let's start from the left. On the bottom, there's kind of like a holodeck-esque tear in reality to suggest that this world is not yet finished. On top of that is a mountain range with a volcano, to suggest the beginning of things (initial planet formation, geographical changes due to active plate tectonics and a hot core). That plume of smoke is coming from a little primitive village. In the middle, on the ground, is a river, both because rivers are important to geography and civilization, but also to again represent how we as a community flow through a lot of different topics.
Above that is another planet, with a moon orbiting it, and a star to its upper right, this part symbolizes our focus on space and physics and all that. There's also a dragon and a spacceship, representatives of fantasy and science fiction.
To the right there are some hills, kind of an antithesis to the mountains to represent erosion and the changes to things over time. Behind the hills is a futuristic city, to match the primitive one on the left. In front of the hills, or really on top of one, we have a man with a spear looking to the sunset with a robot.
Oh, and behind everything there is just a bit of fog, or dust, or something. I just like having that extra layer, but it could represent the unknown, and again the fact that there are parts of this world that are yet to be explored.
I guess this mainly focuses on the duality of beginning and end, but I think it also does a decent job of incorporating most of the things we talk about here.
As for colors, I think there would be some, but as I'm vaguely colorblind I don't tend to worry much about them. I'm thinking pastels and simplicity would be nice; you know, something basic, yet inviting. A calming vista rather than a sharp one, to remind new users that we have some semblance of order we like to keep, and they should really go to the help center first.
But yeah, this just my idea. I don't really know how much symbolism actually works, but I like thinking about it.
An alternate option would be to use my avatar for everything. I would also be on board for that.