To begin with there was the M16. It was introduced with a fixed carry handle with a rear sight that was adjustable for windage and the front sight was used to adjust elevation. Handguards were triangular and the grip had no index finger groove. It had no brass deflector and no forward assist. The barrel was of a narrow profile and featured a three pronged flash supressor. Rifling twist was 1 twist in twelve inches, (1:12). The rifle was designed to fire in semi-automatic and full auto modes.
The M16A1 added a forward assist. Chrome lined bores and chambers were added somewhere in the early days of the M16 as well. Buttstock variations exist as well, Some had trap doors to allow storage of the cleaning kit, some did not. Some feature a fixed rear sling swivel others had one that pivoted fore and aft. Some A1s featured a birdcage flash supressor.
For comercial rifles A1 can mean a fixed carry handle with windage only sight adjustment. They sometimes are slick sided like M16s Some feature forward assists like the M16A1 and others also include a brass deflector like the Canadian C7 version of the M16.
The M16A2 added the brass deflector and a rear sight that featured turn-knob adjustable windage and elevation adjustments on top of the fixed carry handle. The Barrel was made heavier ahead of the front sight base and the barrel profile remained thin in diameter under the handguards to facilitate mounting of the M203 grenade launcher. The rifling twist was made faster at 1 twist in 7 inches, (1:7), to allow for proper stabilization of the heavier tracer rounds that came along to have similar trajectory as the new M855 62 grain ammo. Flash hider was a modified birdcage with an enclosed bottom to prevent dust from being kicked up while firing prone. Handguards were changed to a round profile, pistol grip had an index finger groove, and the buttstock was lengthened and strengthened. The A2 fire control group was modified to do away with full auto fire in favor of a three round burst mode.
Commercial versions of the A2 often feature barrels with 1:9 twist rates adn heavy profiles under the handguards.
The M4 came along as a carbine for airborne troops and is working it's way toward general issue. It features a flattopped upper with removeable carry handle and similar adjustable rear sights to the A2 with less elevation adjustment. It has a 14.5" barrel with cutouts to accomodate the M203 grenade launcher. Flash hider and rifling twist rates are the same as the A2. The Front sight base height was changed to correct sight alignment with the carry hande and for the shorter sight radius of the carbine. Feed ramps were enlarged on the barrel extension and extended into the upper reciever itself to improve reliable feeding during automatic or burst fire. Larger diameter carbine handguards with double heatshields were added, and the buttstock is colapsible. Early versions used three round burst and current production returned the full auto feature.
Commercial versions may not have 1:7 twist, M4 feed ramps, dual heatshields in the handguards, or grenade launcher cut-outs under the handguard. Many are 16" iwth removeable flash supressors to meet BATFE regulations and cannot be fitted properly with standard bayonets. Others feature 14.5" barrels with permanently attached flash supressors of greater length to meet the BATFE regs.
A3 and A4 rifles are 20" barreled rifles The A3 is basically an A2 that has replaced the burst feature in favor of a return to full auto. The A4 is a flat top upper with detachible carry handles like the M4 carbine and may feature Burst or Auto fire.
Commercial clones use either designation to decribe 20" flat top rifles. Same features may be different on them as commercial A2 rifles.
Other commercial differences are that most feature 4140 chrome moly steel instead of the military grade 4150. Many companies do not make chrome lining standard. Rifling twists are more commonly 1:9 twist, and barrel profiles are often different than military rifles made to mount grenade launchers.
Other variations that are not general issue in the military are SPRs which were developed originally as special purpose uppers to give Special Operations troops some versatility in the field to provide precision fire in a compact package. Features include free floated match grade barrel of 18.5 inches on a flat top reciever. Purose built rifles ahve now become Special Purpose Rifles instead of uppers only Variations that you can google are the Mk12 mod 0 and Mk12 mod 1.
The SDMR, and SAM-R rifles are the Marine Corps and Army's, squad level marksmens rifles to add precison capability to the squad level of all units. These feature match grade stainless steel barrels of 20" in frefloated handguards with magnified optics, (ACOG or Leupold).
National Match service rifles used by military marksmanship teams for competition must retain outward appearance of the A2 or A1 rifles but are enhanced to increase the competative edge within the rules. They often feature match grade barrels with fast twist rates to accomodate heavy bullets with long profiles to reach out to 1000 yards. Teh barrels are freefloated in tubes that accomodate the standard handguards. Match triggers are used but cannot be lighter than 4.5 lbs. Finer profile sights with finer adjustments are used.
Flash hiders and bayonet lugs are optional to accomodate shooters who live in states that still retain bans on these features.
I'm sure I missed some details, but thats the summary.