Depends a bit on happiness in the settlement.

High:
-Repair everything that gives a bonus to happiness or law - unless the effects of the particular temple are not needed, and I will replace it with something else (if Distance to capital is more than 40% penalty, it will always be the temple complex that has the max law + happiness bonus).
-Regional Pacification
-Government
-

Rebellious:
-Repair everything that gives a bonus to happiness or law. Exceptions could be high cost unique buildings that may have been damaged in civil revolt, such as the temple of Jerusalem, or the tombs of a Royal family.
-Regional Pacification
-One MIC, usually the one which gives me the best garrison troops. Of course, a MIC that can actually retrain part of my troops has preference.
-Government
-Temples / Game Fields / opting for the most efficient way of increasing the bonuses, and reducing culture penalties.

Note, that basic walls take precedence even over the MIC.