The order for the wires is specified so that the twisted pairs are used as transmission pairs on the cable. I'll be brief here because wikipedia is more eloquent: twisted pair cabling works by sending 2 signals, 180 degrees out of phase over each wire of the pair this enables interference (happens equally to each wire) to be eliminated at the receiver end.
Originally Posted by matt40k
For 10/100Base-T operation the green and orange pairs are used, for gigabit operation all four are. If you don't transmit the differential signal over each wire of the pair then the summing at the other end won't work out.
As for how this affects the cable order at the plug end, 10/100Base-T use pins 1,2,3 and 6 which is o-w, o, g-w, and g according to T568A/B.
Twisted pair - Wikipedia, the free encyclopedia