I would honestly have to say 99% of history. If you got a timeline of human history and marked on it all the periods which you have seen appear in video games, nearly all of it would be left unmarked. I wish there were more games set in the real world that weren't all set in the same places at the same times. And if a developer wants fantasy, not real life, why not try something like Darklands occasionally? That game had a brilliant premise, although I can't really recommend it other than that unfortunately. http://www.gog.com/game/darklands
Also, while some periods are used a lot, there are aspects of them that have been left untouched. Take Ancient Rome for example. We've all seen the military a thousand times, but, as I'm sure anybody with a reasonable knowledge of the classical world will agree,there is so much that hasn't been touched on.
The problem is, while these periods of history are fascinating, you have the conundrum of how to turn them into a game. Archaic Greece may well be a really interesting time to read about and study, but what type of game could you set there that would be even remotely historically accurate? A film or a book, certainly, but a video game is much more difficult. Why are there loads and loads of WW2 games but hardly any WW1 games? Because WW2 had aerial assaults, night raids, beach landings and other, exciting, cinematic experiences (terrifying and horrific in real life obviously, but you know what I mean) which lend themselves perfectly to a video game. What would you do in a WW1 game? Sit in a trench, occasionally go over the top and die. Not exactly what you look for in a good game. I'm not saying developers shouldn't try, I'm just pointing out why many of them probably don't.