MacOS – Dark spot appearing on the Screen , MacBook Pro 13

I use and recommend Shades (free), which can darken the screen beyond the built-in brightness control. If you really want to get it darker, use the built-in shortcut Cmd+Opt+Ctrl+8 to invert the screen colors (same command reverses the effect).

Nocturne (free) allows you to tweak some of the inversion settings.

Given this is happening after a clean install, there are no errors in the log, [EDIT: and the problem is intermittent], sadly I'm suspecting a hardware issue, which coincidentally has occurred near the time of upgrading from 10.5.

I have seen issues like this which were caused by a failure of the inverter board (which generates power for the display backlight).

I would recommend making a reservation at a Genius Bar at an Apple Store and have them take a look. But... this issue can be difficult to diagnose whilst it is intermittent, so perhaps wait for a while and see if it gets worse (which is then not so good for you, but easier on a technician).

In the meantime: a minor suggestion -- instead of holding down the power button when you encounter the issue (which doesn't give the software a chance to clean up), try ctrl-alt-cmd-eject, which should shut down more safely.

EDIT: I forgot one important thing -- try resetting the SMC, since I believe this controls power to the inverter.