This is only the REAL basics so far...
The way I see it, we have a series of civilisations that rise and fall, leaving little or no trace.:
Prehistory - Dinosaurs. Do they have a civilisation at all? That could be interesting.
The Stone Age. This happened as many people imagine it from films and TV and so on, people living in caves and hitting each other with clubs etc.
The Age Of Heroes. We have a prehistoric Heroic Fantasy setting here, with elements of both Conan type stories and more Tolkeinesque stuff going on. Dragons, Elves, Wizards, Dwarfs etc all milling around doing their thing. This goes on for several thousand years. I think that each civilisation should go through the five stages from Illuminatus! - Chaos, Order, Confusion, Bureaucracy, Aftermath. This would allow us to do both traditional heroic fantasy and Discworld style satire of the Beauraucracy stage.
Atlantis also sank around this time.
Biblical times/Egypt/Greece/Rome - again, pretty much as people imagine them. Feel free to create as many pharoahs and emperors as you want, or to mess with the timeline as much as you like.
King Arthur - this is to the Age Of Heroes as the Renaissance was to Ancient Greece in our world, and should be played as such. The Arthurian times end around the same time as Robin Hood existed, give or take a few hundred years.
The Middle Ages exist mostly as a setting for Shakespeare's plays.
The Victorian era onwards should happen more or less as it did in real life. There were more gangsters in the 1930s than in real life and superheroes started appearing then too, but in general life remained pretty much unchanged for most people. By the mid 18th century most of the more odd animals (vampires, trolls, talking gorillas and so on) had retreated to obscure parts of Eastern Europe or Africa, and people had essentially stopped believing in them.
'Now' is pretty much like now today, except that the level of technology in some ways is more advanced. Teleportation and time machines might exist, but if so they're prototypes only, most people haven't even become aware of their existence, and they don't make much difference to people's lives. There's a colony on the moon, and another on Mars, but again these don't really enter into most people's thoughts.
Superheroes exist - there have been 'mystery men' since the thirties, and a few powered heroes since the 60s. There are nothing like as many of them as there are in superhero universes, however, and while superteams exist, people wouldn't expect them to make any real difference to the world.
Roughly 20 years from 'now' we have FTL and first contact with alien intelligences. A hundred years or so from then, there is a nuclear war which devastates most of the earth. However, a few billion people by then live off Earth, and so while the Earth becomes uninhabitable for a while, except by a few roaming tribes of mutants and suchlike, it's eventually repopulated, and becomes one of the centres of the galactic Empire.
The Empire itself goes through two separate phases. In the time of growth, it's high-concept space swashbuckling, a la Flash Gordon or Buck Rodgers, with jumpsuited heroes battling evil space dictators and saving the girl. Later on, it settles down into a more sedate empire, a la the Federation in Star Trek or the empire in Foundation, except with multiple sentient species (humans, vampires, trolls etc) from Earth as well as aliens.
Eventually, the empire crumbles, humanity is reduced to almost nothing, and the Things under the sea, which have been guiding humanity for millennia through The Conspiracy (which involves every conspiracy idea ever) come out. Their breeding program has produced some very tasty meat...
There will be whole alien civilisations too, as well as beings from other planes (faerie, Heaven, Hell and so on). There is one 'true god', but that god has multiple aspects, each of which have multiple identities which can interact, thus allowing elements from any major mythology to share the same stories.
I think this probably works as a very basic outline of a history for the universe, and can be expanded on and elaborated as necessary. I don't want to be too restrictive with the very first posts ;)