Have pop-up screens (My Projects, Compare Progress, Save Script, etc.) open up on the same display as the main program when program is running on a computer with multiple displays.
I've noticed that if I'm running SQL Compare or SQL Data Compare and move it to my secondary display, it still tries to open up pop-up dialogs on the primary display. This can be annoying, especially if it has been a little while since I used the program and I forget it does this and can't spot why program seems to have stopped responding to mouse clicks. Also, when the displays are different sizes (larger monitor attached to a laptop, etc.) the pop-up position can be awkward (have to move pop-up to see buttons, etc.)