What is the usage of the negative voltages on a PC motherboard?
PCs are stuffed with requirements which relate to backwards compatibility - and -Ve rails are part of that.  I'm not sure about -5V, but there's a -12V line on the original PCI bus, so if you want to provide proper PCI sockets, then you need a -12V rail, even if the last person making a PCI card which needed -12V died in 2002.

Then if you want to design a standard power connector pin-out which can be used by people building motherboards with PCI connectors on it, then it needs a -12V rail, or else the motherboard manufacturer needs to start adding power supplies to his motherboard.  So now you have a -12V rail on your power connector even after people have stopped fitting PCI connectors.

Some of these things are remarkably difficult to get away from &mdash; the 'legacy free' PC with no PS/2-style keyboard/mouse connections was being talked about as imminent 15 years ago, but desktop machines still tend to have those connectors.

It just turns out to be cheaper/easier to keep supporting all the old cruft than it does to drop it and clean-up the design. Or perhaps it doesn't, and PCs have sunk under the accumulated weight of all this baggage and people have moved on to other form-factors...