I also noticed that this bonus is not constant per empire - it varies from city to city. For exmaple Japanese capital has 141 culture from "normal" sources and additional about 100 from this unknown source while other cities have +400 or +500 additional culture points from unknown source. Aztecs have the same bonus - much greater in their old cities they founded themselves and much smaller in cities they conquered later.
BUT for some reason player number one in my current game - Victoria, do not have such bonus at all. Her capital city has 61 culture per turn, everything as it should be, absolutely no unfair, unknown points out of nowhere.
EDIT:
I checked old cities of my most developed civs on map:
Asoka - no bonus at all
Gilgamesh - absolutely RIDICULOUS bonus:
233 from normal sources and more than 2000 culture per turn OUT OF NOWHERE.
Qin Shi Huang - very delicate bonus, about additional 10 point per turn.
Genghis Khan - no bonus at all
Suleiman - no bonus at all
Bismarck - no bonus at all
Ramesess - very tiny bonus (about 10 points)
Louis XIV - no bonus at all
Tokugawa and Montezuma - large bonus (from +200 to +500).
EDIT AGAIN:
It's so ******ed I have to literally take a long break from Civ IV. I've checked all cities of Gilgamesh. One of his city gets additional more than 2000 points per turn out of nowhere. Most of his cities get about 1100 additional points out of nowhere. And his capital city... gets only 50 points out of nowhere. WTF!?