You can control video overlay settings with the proprietary NVIDIA driver. (
nvidia-current package, in case you're using the default nouveau driver.) Open System > Administration > NVIDIA X Server Settings. Hit X Server XVideo Settings in the list on the left, and tweak the values on the right to suit your needs. This should affect anything that uses XVideo, such as most media players.
The only issue may be Flash, which could bring you back to square one. It's possible that it does use XVideo (and awesome if it does) but if not you don't have a whole lot of options for that.
Edit: I tried this out myself, and it turns out Flash is not affected, unfortunately. You may have to wait for Adobe to implement XVideo or video acceleration in Flash unless another solution comes up.
However, it is possible that the darkness issues you're experiencing could also be video driver related, though I've never heard of an instance of this on Linux before.