The key is to have any easy way for users to monitor usage, so they can cut back, or get ready to pay more. Also important, is making the process of paying more a pleasant experience. No, you are not "punishing" the customer for using your service too much. In fact, you want to reward them by offering them an upgrade to a plan with a higher allowance, at a substantial discount over the "a la carte" overlimit charge. And, you should find the increased gross revenue rewarding enough to invest in equipment, cables, and peering to keep customers ever expanding bandwidth hunger fed, and your cash flow flowing.
Less important, but nice, is to honor QoS tags from the customer, not you, so that with a smart router (or linux box), they can watch a high def movie (high bandwidth), while chatting on VOIP (low latency), and downloading the entire 50G Fedora distro (batch).