i have never razed a holy city. my understanding is that if you do that, all other civs know and resent you for it, even if they'd never had any cities with that religion themselves?
factors for me in razing vs capturing in early wars are the generally if it has any wonders, if it's well-placed, if it's close enough to me to justify the maintenance cost (can be real important early game), and how close it is to other civs that i don't plan to go to war with soon, since if it was nice enough for civ to settle, another civ might well settle there too.
right before bed last night, i was going to capture Brennus's capital (his last city). i wanted to move it, it was placed ON horses, which i'd rather have pasteurized. i could tell i'd stayed up too late cuz i sat there all mad at him thinking 'you idiot why'd you settle ON them???' and *then* remembered he didn't have AH in 4000 BC, so he had no idea he was doing that, oops my bad. Saladin was nearby tho, same continent and a distance land-wise but he could reach it by galley pretty quickly (and did have one out watching the battle, right there at the spot, warlords obviously so you can't see what troops are on the boat). so i didn't actually finish the battle and raze Bibracte it until i had a settler there ready to settle New Bibracte where i wanted it that turn. i've been cultivating sally as a religious friend and didn't want to have to go to war with him over taking a city i'd rightfully earned!! i really wanted that city spot, as a capital it had of course started with juicy resources in the BFC but the closeness of a rival was a definite factor there too.
i was out killing barbs for exp last night and catpured a 2-pop city. i'd usually have razed it, it had far too much jungle in it, missed the fresh water river nearby to get all 4 resources (but i'd have done that too, eventually worker effort will make the jungle -health will go away) and it was quite far from my homeland. it's in fact closer to alex (who's bound to go crazy sometime, but hasn't yet) than to me, but not close enough to be culturally threatened by him any time soon (which then translates into it never will be, since i will culture it up soon on purpose, including delaying calendar since this is the first game i've ever built stonehenge). the BFC has 2 bananas and 1 dye, i have neither anywhere closer to me, and also a rice that will be surplus for me, and 4 hills for production, so i kept it and we'll see how it goes. it was really well placed, i'd have put it on the exact same square. i've often had cities i captured from barbs develop into killer cities later one ... one recent game a barb city i'd captured thousands of years before became my main naval production city.
maybe i tend to like barb city placement more than the real AI civs is that they don't have to consider things like overlap with their other cities, distance/maintenance cost, how much effort it will be to hook it up to the trade network, etc. i don't know how much the other civ AIs take that stuff into account but as a general rule, going strictly by city placement on the map and not taking into account population or improvements in it, i like barb cities more, go figure. note i mean the BFCs here, and often the barb cities never get enough culture to control their BFC, but they clearly are programed to take it into account.
here's a
link to a thread i started recently about the 'what buildings does it have' factor for the raze/capture decision much later in the game, in case it helps you any. and
another to a thread with more detail about how the game decides what to keep.
+ many culture so no cultureflip
