I'm sure that someone has looked at the "citification" benefits and posted them, but I haven't looked.
Mining a city site and then building a city there "gains" a food sheaf (two food & three shields as opposed to one food sheaf & three shields with Monarchy/Republic); building a city on an unshielded grass gains a shield; building on a plains or shielded grass gains "nothing". (Of course, there is an opportunity cost of time in using these spaces, so I haven't looked at tundra, desert or other "low value" spaces too much.)
Most important in my mind are the associated spaces where the citizens will be (like a four special sweet spot) -- so if a hill or mountain is in the middle, I'll plop two settlers there (first to mine second to settle). Later in the game I'll send an engineer back to transform the mined mountain to a mined hill.