What PaleMantis says is correct. However, if you mean these to be used when you give or present something to someone, the first (Here you are!) is the more normal. An alternative (more American) expression is "There you go!". I have not heard the expression "Here you go!" except to a child, and it is used when setting them off on a swing, or a bike, or something.

There is no real difference and you will be understood. To me "here you go" sounds a little less polite and is more something you will say to a child. "Here you are" can be used in any situation.

In my idea there is no difference and you can also say just" here" :)