It depends.
I believe the darker windows look better on lighter buildings such as the tan on to the right and the grey (skyscraper?) on the left, while the lighter version fits better on dark houses such as the tall one in the back or the one behind the tan building.
Really, I just like the version that provides the most contrast to the building in question.
If I had to choose one of them, I'd use the 2nd version because it doesn't stand out as much, and wouldn't look as noisy from far away.