I haven't studied them enough to accurately assess the policies, so it's just based on my gut reaction.
I like honour, rationalism, patronage and freedom the most. Order and autocracy can also be good, but usually come too late to make much of a difference for me. Which ones I chose depends a lot on my play style of course.
Unless I'm on an island I like to put some points in honour. Not because honour is all that great, but because I find it to be a lot better than the other 2 ancient policies. I try to either put 1, 3 or 4 points in in and therefore either take only one point or max out one of the branches. 50% cheaper upgrades can be game breaking, and double XP is also nice. 15% improved combat rating is also very nice, while I find the last two bonuses to be more meh...
Patronage is pretty much my happiness policy. Maxing out the left side will give a huge boost to happiness. I have never really got all the way to the final right side policy, does it give great people often? Is it worth it? Sounds good, but I hardly ever have enough policies to max it out.
I find the best part about rationalism to be bonus to specialists and bonus to trade posts. With lots of puppy states with trade posts, this gives a huge science boost.
Freedom is a bit situational. It's great on lower difficulties, but on higher difficulties I don't really build any wonders and generally rely more on city and puppet states.
I find liberty and piety to be underwhelming, and tradition and commerce to be very situational. I hear many people talk good about piety, so I guess I should give it another chance. Might work well for cultural victory or Persian golden age tactics.