the penalty is 5% extra science per tech for each city in the empire minus the capital I believe. So the penalty gets worse the farther along the tech tree or the more expensive policies get. Culture is heftier. I think it's 10%. Culture penalties for annexed cities is nothing to help with warmongering, but they also get a science and culture output penalty and cost you maintenance so they can still drag you down if you get too many. Great people costs is based simply on the amount of previously generated ones of the same type. It goes up by 100 each time one is produced in the beginning so more cities can never slow it down. If anything you'll get more great people if you get those new cities working slots quickly. The penalties get less on larger map sizes but the game runs slower. You can try them out and see if you like them--I do.
There isn't a hard and fast rule on city number. But in general, I find that maintenance and happiness costs are such that on standard you can't really make more cities then it will take to make those penalties significant.
Even going liberty on standard/pangaea you will probably not be able to settle more then 10 good cities. And more realistically probably only 7-8 if you are growing your core to stay competitive. 7-8 is fine and you can easy beat any difficulty if you keep them all growing normally each will produce more science then the penalty, especially the jungle cities, mountain cities, and ones running scientist specialists which pay you back with bulbs at the end of the game. Culture cost is bad because you make a lot less culture per city. At 10% I think it's safe to say if you don't want to slow down your culture acquisition don't make more then 10 cities. However, if you take liberty you get a 33% reduction to policy costs which is really significant in counteracting that culture penalty, and if you get a religion or one spread to you that has religious buildings with culture the wide empire can start getting even more then the small empire so it really varies.
