So, here's an example of a thought process I go through when I choose my military policies (it helps to look at each type of policy individually then choose whatever card you really wanted in your thought process but didn't manage to get as your wildcard.
So, am I currently building units, encampments, or walls, or will I want to start building units during my next few turns? If yes, what do I want to build? If I want to build a big army quickly, I'll choose the production policy, saving production time is always great.
Do I have a big army? If yes, that reduction of maintinence cost is really good.
If I don't want those policies, some defaults I go to are +1 movement for units that starts in your territory (gives builders 3 movement points and helps your troops respond to barbarian raids better, which is still very nice in peacetimes) or +1 ammenity for each unit garisoned in a city (always useful if you have the extra units to sit there or are at peace).
Then, by the time I've considered those categories, I've usually gotten a military policy in place. Then I go to the economic policies and do a similar process. Look at your empire. Do you want a builder wave or a settler wave? If you do, take a builder or settler policy. Do you have lots of specific districts? If you do, then take a policy that makes these districts better. Don't have many districts and aren't creating builders/settlers? +1 production per city is pretty nice. God king is good until you get a pantheon, then I don't use it much after that.
The diplomacy card is usually relatively simple to fill. Just choose the one that suits your empire. You want to place an envoy in a city state you don't have any in yet? Why not make it two envoys. You don't want to do that? Get more envoy points, they're great. Want more gold? That +gold per envoy policy gives out a lot of gold and is pretty good.
Then, for the wildcard slot(s), choose either a great person policy (if you want a great person, the great prophet policy is almost necessary if you want a religion), or choose a policy that you looked at earlier and wanted but didn't have the space to take.