There have been over 150,000 upgrades/changes from the inception of the M-16 to it's current production. It is the most tested and reliable weapon platform in use today.

Switching to the civilian version it mostly mimicks the military version, except of course being semi-auto and some changes in the bolt and trigger group. I am not taking into account barrrel contour/ profile or length.

The biggest and noticable changes to me are:
A1
5 position front site adjustment wheel
A1-style rear site...harder to adjust
Triangular hand guards
Never had tactical handguards with rails

A2
Addition of a forward assist to the bolt
4 position adjustment front site wheel
A2 800 meter rear site
Round handguards w/ addition of heat shields

An A3 M16 is not to be confused with a A3 AR-15
An M16A3 is a full auto/semi auto...no 3 round burst

A3
Upgrades of A2 plus the following
Removal of carry handle in upper receiver casting while adding a rail where the handle used to be.
Optional carry handle available

M4
All upgrades of an A3 plus the following
Cuts made in barrel extension lugs acting as a feed ramp
Different profile barrel
6 position collapsable stock as standard equipment

Obviously I have missed over 149,985 upgrades....please excuse what I've missed.
If anybody else wants to add more feel free....I will not be offended.