There are some civic patterns that emerge. When i focus on specialists i run Representation, Bureaucracy, Slavery/Caste, Mercantilism->State Property/Free Market, All but Pacifism most of the time, but jump around little more based on teching vs war. When i run cottages its more one time transitions hereditary rule -> universal suffrage (eventually), Bureaucracy -> Free Speech (eventually), Slavery -> Emcipation, Mercantilism->State Property/Free Market, All but Free Religion most.
No matter how you get science (commerce vs specialists):
You might look into Bureaucracy in the legal line. Pretty much no matter what you do in the game the capital is going to be a dominant city, and Bureaucracy cements that for most of the important game deciding turns. You would switch out of it for specific needs.
Nationhood to draft or vassalage to build an army.
Free speech isn't a lock unless you have enough towns in your empire to out produce the +50% base commerce capital towns produce in Bureaucracy.
Government:
If you get science from specialists Representation is basically a whole game civic. If you don't have the pyramids to use it the whole game then Hereditary Rule is a placeholder until you get to mid-late game to unlock Representation.
If you get Science from Cottages then Hereditary Rule should dominate most of the game to grow cities vertically to work more cottage tiles. Eventually Universal Suffrage makes more sense when you can afford rush buy (might save up for or wait for Kremlin).
Labor:
Everyone but serfdom is good and has a use.
Slavery and whipping is the key to the early game and can be used the whole game, but tends to get in the way of running cottages and loses its efficiency on large cities 10+.
Serfdom, doesn't offer much benefit. More workers can also get the tiles improved faster.
Caste System is usually a dominant civic for specialist/food/hammer heavy economies, at least for those not addicted to slavery.
Emancipation i guess is what a cottage economy ends up in. If you have mostly towns anyway shouldn't you be running something else?
Economy Civics have an interesting affect on the game and tech rates.
Mercantilism is good for most of the game in a specialist focused economy.
Free Market boosts commerce for you and your trade partner, which can be good and bad. I usually only switch to this when i am ready to found a corporation or two.
State Property, almost always run this as soon as i get it. No matter what your economy is like usually the maintenance savings provide a large benefit. If you have workshops they become super strong at this stage.
Environmentalism, Rarely get to here and rarely need the health, so haven't used it. State Property or Free Market are usually better.
Religion, almost all useful and situational.
Organized Religion, good during early build out of infrastructure. Expensive to run, so usually switch out to something else. Often come back to it for Spaceship parts.
Theocracy, Run a lot of the game for heroic epic and iron works cities to pump out good units.
Pacifism, run early game and during most golden ages to pump out great people when they are important (early).
Free Religion, sometimes spend most of the game in this for diplomatic reasons.
.
I wish Serfdom were better balanced - the more viable civic choices, the merrier. (If I had to balance it... maybe I'd move it to Monarchy?)
, I generally advocate the slavery <-> serfdom constant switch if spiritual (or own the Rententor -- but this wonder comes in so late it is unlikely for you to still be in slavery mode). The best thing about this is not you are in serfdom, but is you are not in slavery, hence no annoying slave revolt. Serfdom is the best choice to switch to, since it provides some benefit and is low upkeep.
