While we're on the subject of special editions and, for the sake of the OP, there were a few that are worth noting because they had or had the potential for, some actual meaningful mechanical differences. Again, use chris' excellent
Trim Packages and Special Editions post as a detailed reference, but...
The
SE. This was a base model that only came with the 4 cylinder engine (2.4L or 2.5L) which, for a dedicated off-road vehicle, is not a huge deal but, for a daily driver, they just don't have the power to go highways speeds; especially if you go with oversized tires.
The
Sahara editions. These had the OPTION for a Dana 44 rear axle and, from what I have seen in for-sale listing, many of them did. They also had fender flares that were painted the body color (certainly cosmetic, but a popular thing).
The
Unlimited (a.k.a.
LJ) edition/version. Made from 2004 to 2006, these are highly prized as, due to their longer wheelbase, they can hold more, tow more, and are better for setting up for overlanding. They are also better in certain circumstances off-road...a big point of debate
The
Golden Eagle,
Rocky Mountain, and
65th Anniversary Editions all had Dana 44 rear axles.
The
Rubicon version. Only available from 2003 to 2006, these are a
major mechanical/offroad upgrade. They came with larger tires/wheels, 4.10 differential gear ratio,
4:1 ratio transfer case, minor rocker armor, and electronically-
lockable Dana 44 axles in both rear
and front.
And, finally, what is considered by many to be the ultimate "Holy Grail" of TJs; the
Unlimited Rubicon or
LJR. This version, only available from 2004 to 2006, had all of the attributes/upgrades of the Rubicon and was based on the longer Unlimited/LJ chassis.