You'll need to enable QoS. Under classifications there are "Layer 7" settings. It probably won't have all the applications you want, but it's a start. For those not listed, you'll need to research them and find specific port numbers to classify.
You'll need to create different classes. Check out the link below for an introductory guide to QoS on Tomato. http://www.decimation.com/markw/2007/10/03/tomato-qos-setup/