The suns rayes are considered to be basicly paralell when they aproach the earth because of the earth's grate distance from the sun.

 

If so, why then on a broken clowdy day the sun rays as they punch through the holes in the clowds are far fron paralell ?

The sun's rays striking the earth are approximately parallel; the sun takes up about a half a degree, so that light would be parallel to a half of a degree. The light you observe coming through a cloud are going to different spots so there's the issue of perspective — parallel lines going to/coming from a distant point appear to converge in the distance. Like railroad tracks going off into the distance, and you are standing between them.

 

http://en.wikipedia.org/wiki/Crepuscular_rays

Would a lensing effect from the atmosphere also apply?

they only appear to be non parallel.its to do with the way humans percieve the world. this peculiar phenomenon caused intelligent people to believe that the sun was much closer than it actually is a long long time ago.

 

the are called crepuscular rays. http://en.wikipedia.org/wiki/Crepuscular_rays

 

this explains it better than me.