That's interesting, these 6 civs today have more than 100 votes each, a top 6 listing per se: Iroquois, Poland, Austria, Israel (mostly ancient I think judging ppls comments), Hittites, and Polynesia. Pretty much in line with most of my suggestions.
I would call "ancient" Israel by the name of Judea, the Roman name for the area, but that's just personal preference. The name Judea, being used in the Classical period, really strikes home the older civ and not the new one. Like whenever people see "Ethiopia" in the game, they automatically think of the modern country with a pathetic economy and standard of living and wonder why its in the game, and don't think of the history of the region (that's why I favor "Abysinnia for that country).
If anything, I would get rid of the "Native Americans" and then add the Iroquois in. The representation of all "Native American" tribes as Plains Indians--let's face it, totem poles, Dog Soldiers, and Sitting Bull, that's the effect they were shooting for--is a horrible stereotype. Not to mention its confusing with having the Native Americans as well as the Inca, Maya, and Aztecs, all of whom are "Native Americans" as well... The Iroquois were actually a nation with representation from 5/6 tribes, built settlements, etc. and are more appropriately represented with Civ mechanics.
Austria and the Hittites were previous inclusions (Austria the unofficial "extra" Civ of Civ3) that I figured would get back in with BtS. Although I would replace the HRE with Austria, since the Austrians dominated the HRE for centuries. Hell, the colors for the HRE are already the colors of the Habsburg royalty. No problem there!
Polynesia doesn't strike me as a really viable choice. If anything, pick a particular tribe--be more specific. Referring to a generic European term for a group of people spanning thousands of square miles of ocean and small islands doesn't fit the Civ model for civilizations. Poland, however much there is clamoring on the boards for them, is a long shot even for the 2nd expansion pack to a Civ game. I'm not opposed to them personally, but I would put in Austria and the Hittites first.
If I had to pick a list of suggestions, I would select the following as first choices:
Austria
Hittites
Judea
Iroquois
...with Poland being the honorable mention.