Duh. You change the version number whenever you allow a change to any module to escape your tight little grasp.

In the case of emergency changes, try to change the version number in a way that won't conflict with the next version that the real author of the module is likely already working on and will be releasing soon, before he notices that you've upgraded out of his control. I usually do this by incrementing by a smaller-than-usual amount (such as appending "001" to the end).