Why is -12V needed on an ATX power supply

Solution 1:

AFAIK there are 3 type of devices on a motherboard that require -12V.

1. RS232, RS485 ports without build-in circuitry for generating the negative voltage.
   These are starting to become very rare... Haven't encountered any for the last 5 years or so.
2. (mini-)PCI slots. They are slowly being phased out in favor of PCI-e, but there are still a lot of new computers made that still have them.
3. Some high-end sound-cards require -12V as a reference voltage. These are usually powered from a PCI slot, which brings us back to point 2.
   (There have been a few motherboards that had such a card integrated in the motherboard itself.)

PSU manufacturers can't know in advance if the motherboard will actually need the -12V so they will keep adding the -12V line to the plug as long as the ATX standard requires it.
And it is not only a matter or whether it is needed or not: If you don't include it, your PSU will not be ATX compliant and you can't sell it as such.

Solution 2:

It's a deprecated rail much like the -5V one once was. It used to be used to power the RS232 serial ports, but most newer equipment can supply its own negative voltages internally.

So basically, it's useless for today's equipment.

Source

EDIT: As it it was pointed out, the -12V rail is also used in the PCI specification to power it. As PCI is being phased out in modern hardware, the -12V rail will likely follow in its footsteps.