What is the reference point for AGL? I am about to start my PPL soon (still flying in FSX) and I do not understand one thing. As per FAR 91.159 if my altitude is above 3000' AGL I must maintain certain altitude depending on my course, BUT what would be my reference point to know that I am above 3000' AGL? Departing airport? MEF from chart? or just look out my window? Thanks!
FAR 91.159 speaks for itself.  The reference point is directly below your current location.

There are other regulations that use "AGL" (sometimes stated as "Above the surface") as a reference (see FAR 91.155 or 91.119).

As a side note, FAR 91.159 is used to mitigate the risk of midair collisions but not at the expense of prohibiting necessary close to the surface operations (e.g., helicopter EMS, telephone line patrol, crop dusting).