What types of fault protection is recommended for low voltage power supplies?
You should consider:


Fusing on the AC side of the power supply to protect for possible transformer primary shorts and secondary current overload.
Crowbar over voltage detection on the output that is an SCR that shorts the output of the bridge rectifier such that it causes the AC side fuse to blow.
Current limit detect on the output. Some switching controllers have this built in but if yours does not then select one that does provide this functionality.
AC spike filtering at the supply input using common mode choke filters and MOV type device surge absorber component.
Thermal cut out device that works to activate the crowbar to blow the primary fuse of the transformer core gets too hot. 
Thermal foldback in the switching controller that shuts down the controller in case of too high of temperature. Some switching controllers have this built in but if yours does not then select one that does provide this functionality.