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