Very good question
its my ongoing project for now .
there is 2 steps to secure your software
first one is to create a callback script and integrate it into your software .
which mean each time user submit a form or click a link in your software it will send a call for your management script with the serial number and it must send back an approve or error in case of fail and you must set your software to stop in case of fail .
the second step is for non-compiled language or scripting languages just like PERL - PHP and Python
there must an encryption method to hide your codes because if any programmer looked at your code he will easily get ride of the callbacks functions
and to be honest there is no %100 secure way to encrypt your code but you still have ways to make it harder to be reversed to the source code
there are 2 ways to encrypt the code
first one is free using eval and base64 encryption or encoding method and it doesn't need any server modules to be installed in the client side and this one is as easy as piece of cake to break
paid encryption tools like ioncube and zend encoder they both need modules to be installed in the client server side (mostly installed by all hosting companies)they are hard to break but still no impossible to break them