What is the best way to avoid that an application is copied and used without the owner’s knowing?
Is there any way to trace the usage? Meaning periodically the application communicates back, with enough information so that we can know where it is, and if it’s legal. Next thing, of course, shut it down, if it’s not legit.
Hardware dongles are the best way if you are really concerned about piracy IMO. Check out the big industrial CAD/CAM packages worth thousands or tens-of-thousands, or the AV/Music production software, they virtually all have dongle protection. Dongles can be emulated or reversed but not without a significant investment in time, a lot more than just changing a few JEs to JNEs in your assembly.
Phoning home is not the way to go unless you are providing a service that requires a subscription and constant updates (like antivirus products, for example) as part of your business model. You need to have a bit of respect for your users and their privacy. You might have perfectly innocent intentions but what if a court ordered your company to hand over that information (like the US government is doing with Google and its search terms) - would/could you fight it? What if you some time in the future sold your company and the new owners decided to sell all that historic information to a marketing company? Privacy is not just about trusting a company not to abuse your data, it is trusting that company to go out of their way to protect your data. Which is pretty far down the list of priorities for most companies. So basically, the monitoring users thing is not really a good path to go down.