Anyone know what civic's work best for taking and holding enemy city's in the late game?

The government civics all have different qualities. If you're trying to keep a large, culturally varied civ together in the end game, you're probably best off with Representation or US as your government civic. If you want to keep the cities, improving your culture in them is also a must and so Free Speech can help (buy culture buildings if running US). In war, Police State is still useful as it does help quell rebellions, but any that do occur are likely to be more violent because of the repression. Once Representation you have discovered, Hereditary Rule becomes a less stable choice as people yearn for freedom.

Religion can also be tricky ... if you have a single, dominant religion in your main cities then you can almost guarantee homeland stability by running Theocracy. However, it can make keeping new cities with other religions or other holy cities quite difficult... Theocracy is a major win if your state religion is the only game in town and can still be a good choice if there are a couple others, just be sure you spread your state religion everywhere and bring missionaries in your invading armies (this is a Theocracy!). Owning your holy city is also a boon under Theocracy. If you have many religions in your empire, then you'll probably want to avoid Theocracy for sure and maybe Organized Religion if you don't want to piss some cities off.

Those are a few tips.

I generally use Hereditary Rule as a large number of soldiers cancels out its negative reprecussions and are always handy if some misguided individuals pressume to interupt my rule. Police State is usefull in a war as its posistive and as such lessen the attempts of your conquests to call for independance, as does Universal Sufferage and representation of course, Despotism is really usefull if yourve got a colony youd like to be rid of, when combined with high taxes.
Nationalism doesnt give a negative response and adds to happiness and the happier the people the less likely they are to cause problems.
With religions as long as your state religion is in a city, then your fine in a minority religion turns up, as long as there are no other problems with your state, If however the slaves start causing a problem have a failing economy or lose a war the minority religions tend to kicj up a fuss, but enough soldiers tend to prevent most problems.

It always pays to wait to see if a revolution in another state has a chance at winning before striking any deals with them. And if you do annoy someone, dont concour them entirely but leave them behind as a city state or wandering scouts so that next time a revolution occours it wont be them with their negative predisposistion towards you.

I would firmly sugest that a lot of money and a strong home guard can keep most empires shiny.