gen1's have hydroformed plastic they dont have a lip where the color meets the black rocker panels. other than two that i know of, their all red.
they have 2 piece floorboards, the cup holders come out. their flywheel is machined steel, their transmission shafts are steel the battery sits long ways, they have brass plugs and grommets to hold on the hood and the engine service cover.
old gen ones have a hole in the front center of the bed (later ones dont)
the front body is all one piece (no removable pan) they have softer springs,
gen 2's have injection moulded bodies in red or green, they have quarter turn fasteners for the hood and engine cover, they have steel transmission shafts they have cast flywheels they have the lip at the bottom of the body where it meets black, they have two piece floorboards with honeycomb in it. they also have a different skid plate. the battery sits longways (opposite of gen1's) and they have a better designed but smaller storage compartment under the seat
gen3's have a welded in hitch, their spring retainers are made of steel instead of aluminum, they have powdered metal transmission shafts, they have an improved cv joint in the rear outers (maybe the fronts too, not sure) they have a front air/mud/water blockoff kit. (some gen2's have it too) they have a lid on the storage compartment. they have a stiffer throttle spring and a new eccentric in the throttle body
they have a different gas pedal (all metal instead of plastic and metal)
09's have everything a gen3 has plus a different frame. the frame has 4 gussets and a crossbar up front in the rear there are two wing gussets, a boxing gusset on the front upwrights, and lips on the upper shock ears, their voltage regulator is up front instead of under the seat, they have a cutout in the floorboard under the gas pedal, they have a differnt muffler and more heat shielding, their bed plastic is missing some holes.
some have the rapid reaction clutch (after 8/31) instead of the roller secondary clutch..
that's what comes to mind as i remember it
but i liked the first answer better