I just laid 1200 sq ft of laminate and 300 sq ft of marmoleum click. I laid the laminate in the correct direction and I laid the marmoluem (12X36 planks) opposite of how light enters my room because it was just a lot easier.

The reason is seeing the seams and it is quite true. I can see most of my seams on the marmoleum that run in the opposite direction of the light and I can't see the seams that run in the same direction as the light.

I think this is only important in laminate if you use a type of laminate that is wider and is meant to represent 2 or 3 wood planks wide. Then you would see the seams every 3rd plank or so and it wouldn't be a good visual effect. I used single plank laminate so each board looks like an indivdual wood board so it doesn't matter if you see the seams, you are supposed to.

This only applies to floating floors. If you are nailing down hardwood, it generally runs in the opposite direction of your floor joists for floor stability.

For laminate it goes with the window just for aesthetics. Hardwood flooring should run perpendicular to the floor joists or on a diagonal for stability.
I would recommend that you lay out a few rows to get a feel for it and go what direction seems right to you. Usually this happens to be perpendicular to the joists.