Ok I found a post from YMAN that explains it better than I.
All credit to YMAN
"All multimeters will have a DC Voltmeter, set your
multimeter to that. First turn on the comp let it sit
for a minute, before putting any load take a
measurement (as follows). Be carefull to not short
anything out, carefully stick the prongs into an
open molex.
4 WIRE DRIVE MOLEX
Red Prong (+) | Black Prong (-)
------------------------
Red ................. + Black = +5.00 Volts
Yellow ............. + Black = +12.00 Volts
Then place the system under load, you can do this
with a burn in program if you like, and test again,
record the results. If you want to check the 3.3v line
stick the prong ontop the ATX molex, while pluged in.
That might sound funny, but just stick the prongs on
the metal inside the hole corresponding with the wire.
The colors for +3.3v are orange and black. These are
the there main lines that you should test. I will also
list other combinations in the ATX molex below.
20 Wire ATX Motherboard MOLEX
Red Prong (+) | Black Prong (-)
------------------------
Orange .......... + Black = +3.3v
Purple ............ + Black = +5.00v (5VSB)
Yellow ............ + Blue = +24.00v (Mass Fan Overclock )
Red ................ + Blue = +17.00v "