Male or female header on PCB?

My theory is that male headers are less likely to suffer damage by contamination since everything is "out there" and visible. Use the shrouded kind for more protection.

The females, when part of an IDC cable, are more easily replaced if they fail, rather than trying to replace a part on an expensive multilayer PCB.

You will find most products where there was a choice such as IDE disk drives and PCB motherboards will agree with this choice.

There is no standard. Male pin headers on PCBs got their start in the electronics world back when ribbon cables became popular. These cables were equipped with 0.1" pitch female socket connectors which mated with male pin box headers. Over time many applications eliminated the shrouded box header in favor of the open male pin header due to cost and space savings reasons.

These days there are so many choices it really becomes a case of finding the connection technology that best fits the packaging concept for your electronics gadget.

There's not a standard, but a good rule of thumb is to think about would happen if someone untrained took hold of the board. For example, mains wiring is always a socket in the wall so it is impossible or difficult to touch a live wire accidentally. If there is power being supplied by one side, I would generally make that a socket (female). Cost wise, male tends to be cheaper than female, so if you're doing big numbers that may also be a consideration for you.