Can someone explain to me what Mil Spec means, and What the differences between A1,A2, etc?  
Thanks for the help.

Mil Spec = Military Specification. Should be self explanitory. It simply means that an item meets the specifications such as design, material and construction set forth by the military customer. Military specifications are usually very strict and detailed.

I know that somewhere on the net is a list of the changes between the M16A1 and the M16A2
It goes something like this;
M16A2 barrel has a rate of twist of 1/7 A1, 1/12
M16A2 barrel also is heavier from the front sight assy forward, although the increase in diameter begins under the hand guard.
Speaking of hand gaurds, the A2 has round handgaurds that are interchangable. The A1 has triangular handgaurds that are made for right and left.
The A2 has a combination flash suppressor/brake. The A1 has a flash suppressor
A2 has a square front sight post, A1 is rounded. Both are adjustable for elevation.
The A2 rear sight is adjustable for windage and elevation. The A1 is adjustable for windage only. The A2 rear sight apreture is larger than the A1.
The A2 upper receiver has a brass defecltor built in.
The A2 has a beveled hand guard retaining ring (AKA Delta ring). The A1 is straight.
The A2 butt stock is 5/8th" longer than the A1 and has a fully checked butt plate.
The A2 pistol grip has a finger groove molded into it.
The A2 has improved stock materials. A relatively modern polymer as opposed to 50's era plastic for the A1.
The A2 has a spacer inside the butt stock to secure the stock to the buffer tube since the buffer tube is the same length for the A1 and A2. Accordingly, the A2 has longer stock screw than the A1.
The A2 has a reinforced lower receiver at the stock extension.
The A2 fire control parts allow for safe, semi and 3 round burst fire. The A1 safe, semi and full auto fire.

That's all of the relevant differences that I can think of.

Now, if I wasted all that tying just because you wanted to know what A1,A2,etc. means rather than the differences between the M16A1 and M16A2, I'm going to feel pretty foolish. However, A1, A2 etc. simply means that the product has had revisions, modifications, improvements, whatever you want to call them.