I've had this problem too and it has perplexed me what could be the cause. After some thinking, and inline what others have said, it usually happens when firing up an app or switching between apps.
My guess is that this happens when OSX is switching graphics cards. This is entirely my theory so lets see if it holds water.
The mouse cursor on OSX is drawn directly by the graphics hardware (hardware cursor acceleration), as with most modern systems. Maybe there is a race condition where the cursor overlay doesn't get mapped to the new graphics card before the switch happens, so the OS switches to the new graphics card before the cursor overlay is ready. So my guess this problem only occurs on systems with discrete video cards (NVIDIA, AMD) alongside the internal (Intel GMA) one. Systems with only one graphics card probably don't see this problem.
After browsing through this thread, the users who have included system information all have discrete graphics cards in their system, which confirms this theory. Likewise, my system is a 15" MacBook Pro Retina Mid-2012 with an NVIDIA GT650M discrete graphics card running OSX 10.9.5.
If a user with a single (integrated) graphics card is also seeing this problem then i'll eat my words 🙂
Here is a test and possible solution, if you have a system with discrete graphics, in System Preferences -> Energy Saver, untick Automatic Graphic Switching and the problem should go away. This forces the system to always use the discrete graphics. Not a great solution though if you are using your mac primarily on battery power as the discrete graphics uses more power.
A proper solution would be for Apple to fix the issue in the automatic graphics switching (gMux) implementation.
Cheers,
David