Washing machine on a very cool programme. Remove the footbeds. Set the machine to extra rinse and - importantly - throw in a couple of old towels to keep it all in good behaviour.
Just don't pop them in the tumble dryer, this can cause trainers to shrink... apparently...
As a road runner I was always told not to wash my shoes in a machine anyway as it would destroy the air/gel sole thingies and shrink some of the fabric... So I used a sponge and some water.
I stick mine in a pillow case with the footbeds outside the shoe and a couple of lwashing up powder tabs, one in and one out Pillow case stops them getting scratched etc.