Why is there a -12V rail for ATX
-5V was the back-bias voltage for 3-rail DRAMs, in the era of 16kbit DRAMs. These used 5V for the interface, 12V to power the storage, and -5V to provide negative bias to the chip substrate. Without -5V, all 16384 storage transistors turned on at once, pretty much shorting the 12V supply to ground and destroying the chip. 

You needed to ensure the -5V supply was working before starting the 12V supply. However as it supplied a bias voltage, it didn't need to source a great deal of current; 5ma was enough for a whole 64k memory! (the 12V supply was somewhere close to an amp)

Later DRAMs (starting with the 64kbit generation though there were some 16k versions) generated their own -ve supply with an on-board charge pump - and possibly still do, for all I know. These were already coming into fashion as the PC started to take off, but were possibly still more expensive...

-12V was necessary for proper RS232 serial port levels; I can't think of any other purpose for it in a PC.