string is an alias in C# for System.String.
So technically, there is no difference. It's like int vs. System.Int32.

As far as guidelines, it's generally recommended to use string any time you're referring to an object.

e.g.

string place = "world";

Likewise, I think it's generally recommended to use String if you need to refer specifically to the class.

e.g.

string greet = String.Format("Hello {0}!", place);

This is the style that Microsoft tends to use in their examples.

It appears that the guidance in this area may have changed, as StyleCop now enforces the use of the C# specific aliases.