Which specific version of 10.6 are you running? Are you able to boot your system at all, or does it stop at the point where it shows you the blinking folder with the question mark?
That blinking indicates it can't find a valid System to boot from, so there's a problem somewhere. These things don't commonly appear when you shut down after a program becomes unresponsive, so what else did you do that might have caused this, and exactly how did you shut down your Mac?