Do you need to run the motors in one direction only, or in forward and reverse?
If in one direction only, then it's easy, you can control each one using a mosfet driven from a PWM pin.
If in both directions then you need an H-bridge per motor. There are dual H-bridge chips available. Pololu makes good motor controllers, for example this dual motor controller Arduinio shield: http://www.pololu.com/catalog/product/2503.