[droz]

Have your application periodically register with a registration service and monitor for excessive use. If you detect something, call up the customer and ask what's going on and present your data. Tell them they are not licensed to run unlimited number of instances and they need to pay up. If they don't, have a built-in shutdown command that you can issue to the software instances that are unlicensed.

[chrisdew]

Do you think "phoning-home" would be considered bad behaviour?

Are there other applications which already do this?