Here is list of TJ Model changes by year. 2006 may not be a complete list.

2006

New Exterior Colors: Solar Yellow Midnight Blue Discontinued Exterior Colors: Electric Lime Green Patriot Blue

2005

New Exterior Colors: Impact Orange Deep Beryl Green Pearl Discontinued Exterior Colors: Solar Yellow Shale Greeb Sienna Pearl Coat 6-Speed NSG370 manual transmission replaces the 5-speed NV3550 & NV1500 transmissions in all models 6 forward 1 reverse Max torque input 272 ft/lb 1- 5.014:1 2- 2.831:1 3- 1.789:1 4- 1.256:1 5- 1.000:1 6- 0.828:1 Reverse 4.569:1 Weight 40.5 kg SE gets 3.73 axle gears in place of 4.11′s/4.56′s Sahara Edition Discontinued Second soft top on Unlimited, called “Easy-Folding Soft Top” now an option. (Dual tops still not an option on the Unlimited.) New Premium H-Package on the Unlimited model features unique 2-tone cloth seats, silver painted center stack and instrument cluster bezels, bright grille and body color fender flares. Optional six-disc in-dash CD changer system that arrives later in the model year.

2004
New Exterior Colors: Solar Yellow Lime Green Discontinued Exterior Colors: Inca Gold Intense Blue Trail Rated badges The Canyon wheels in the 30″ package are now “Ravine” wheels. Can be purchased in the U.S. with right-hand steering The standard AM/FM Tape is now a CD. There is a standard spare tire cover that comes with the 30″ wheel/tire package now. There is a new “cubby bin” in the center “stack”. Willys Edition: Exclusive Moss Green exterior color Camo and black seats Unique “WILLYS” decal at cowl side Diamond-plate sill guards painted Dark Green Body-color fender flares AM/FM stereo radio with CD player and seven speakers (includes subwoofer in center console) – no extra charge 4.0L Power Tech I-6 engine Tow hooks Fog lamps Full-size spare tire with matching wheel Columbia Edition: 4.0L I-6 Engine 15-inch graphite painted aluminum wheels Unique graphite fender flares Fog lamps Columbia badging Dark Slate Interior Khaki two-tone seats with the Columbia logo Silver painted instrument panel accents Available in Black, Bright Silver, Flame Red, Solar Yellow and Patriot Blue Complimentary Columbia Bugaboo® parka featuring a zip-in Chehalis or Shoshone fleece vest Rocky Mountain Edition: (Nearly Identical as Columbia Edition Except:) 4.0L I-6 Engine 30 Goodyear GS/A Tires on 15×8-Inch Alcoa Cast Aluminum wheels w/ full size spare Unique graphite fender flares Fog lamps Rocky Mountain Edition badging Dark Slate Interior Idential two-tone seats as Columbia Edition, but with Jeep embroidery replacing Columbia logo Silver painted instrument panel accents Available in Black, Bright Silver, Flame Red, Solar Yellow and Patriot Blue Diamond sill plates Tow hooks Dana 44 rear Introduction of Unlimited Model (2004 1/2): 10″ longer wheelbase 5″ extra rear overhang Additional 13 inches behind the second row of seats (doubling rear cargo capacity to 29.5 cubic ft.) Passengers in the rear seats pick up an additional two inches of leg room, and can now access the area with tip and slide seats. 3500 lbs. towing capacity (Extra 1500 lbs.) New Sunrider soft-top, which lets drivers open a sunroof or take the entire top down More sound insulation Revised springs/shocks as well as an additional cross member out back to ensure an improved ride and no loss of structural rigidity
2003
New Exterior Colors: Bright Silver Metallic Light Khaki Metallic Inca Gold Pearl Coat Intense Blue Pearl Coat Discontinued Exterior Colors: Silverstone Metallic Solar Yellow Steel Blue Pearl Coat Amber Fire Pearl Coat Exterior Labeling: On Sports, the word “Sport” now appears at the top of the fender where the word “Wrangler” used to appear. On Saharas there’s a brand new Sahara logo (much more discrete) that appears about where the “4.0L” used to appear on early TJs, roughly where the “Sport” label appears on 2002 TJs. Rubicon has RUBICON label on hood. New Interior Colors: Dark Slate replaces Agate Khaki replaces Camel Khaki color for Saharas instead of green trail cloth Soft Top Colors: Dark Khaki replaces Tan Seat Changes: Additional 20 millimeters of rearward travel Taller seat backs Softer seats Seats are lower sitting (more like a car) Lever on the side of the front passenger seat for easier access to the rear. Rear seats are equipped with the LATCH (Lower Anchors and upper Tethers for CHildren) New fold-and-tumble rear seat — release now on the top center of the rear seat and a new spring mechanism helps it fold and tumble easier than ever before New 3-ply Soft Top that is as quiet as the previous 4-ply NOTE: Change in driver’s side window: male zipper is now on window, female zipper on the top, previous years was vice-versa Plastic windshield trim (Interior Upper Head Impact Protection to meet 2003 federal standard?) Trim on back of hardtop and vents removed (vents added to tailgate) New interior electrochromic rearview mirror with map lights, temperature and compass display A new exterior mirror design reduces vibration, while increasing stability and durability. Shorter, fatter, and all plastic Now “ratchet” out from the body rather than swing out in a smooth motion. Doors – the key cylinder is now chrome instead of black Dashboard redesigned, openings for the radio and HVAC controls are now oval rather than rectangular New 4-spoke vinyl steering wheel for SE and X models New 4-spoke leather-wrapped steering wheel for Sport, Sahara and Rubicon models Smoker’s Package optional on all models On-Board Refueling Vapor Recovery (ORVR) Additional power outlet on the dash New flush-mounted AM/FM cassette radio with CD changer control New flush-mounted AM/FM compact disc radio with CD changer control Replacing the optional sound bar, new standard corner pods located just behind the b-pillar on both sides of the vehicle house interior lamps, providing theater lighting and optional speakers Energy-absorbing foam is added to the sport bar 4-wheel disc brakes optional on Sport and Sahara 42RLE 4-speed automatic option New transfer case skid to work with new 4-spd auto (lower ground clearance) Jeep Wrangler SE Changes: NV1500 five-speed heavy-duty transmission. Also used on Jeep Liberty, this transmission gives Wrangler a synchronized reverse gear and improved shift quality in cold weather. 4.56 gears available with SE and 4-speed auto. Jeep Liberty’s 2.4-liter Power Tech I-4 replaces the 2.5-liter I-4 as the standard engine on 2003 Jeep Wrangler SE models. This 2.4-liter engine provides an estimated 150 horsepower at 5,200 rpm and 165 lb.-ft. of torque at 4,000 rpm, representing a 25-percent increase in horsepower and an 18-percent increase in torque. This increased power and torque is achieved through the use of aluminum cross-flow cylinder heads, dual overhead cams and a four-valve-per-cylinder design. The new 2.4-liter engine is quieter, more fuel-efficient and engineered for longer life and ease of maintenance. Introduction of Rubicon Model: Tru-lok selectable pneumatic lockers, activate in 4-lo and under 10mph, engaged until out of 4-lo or deselected Limited slip in rear when not locked NV241 Rock-Trac 4:1 transfer case — fixed yoke Heavy-duty driveshafts with 1330 universal joints Dana 44 Front (Dana 30 outers) 4.10 gears Goodyear Wrangler MT/R LT245/75R16 (31″) Tires 16-inch, five-spoke aluminum wheels Diamond plate rock rails Rubicon Lettering on Hood 4-wheel Disc Brakes Apex Edition: Special hood emblem Special seats Freedom Edition: Body colored fender flares Special side badges Outlined white letter P225/75R15 Goodyear all-terrain tires mount on 15-inch chrome wheels. Standard soft-top with full metal doors, fog lamps and tow hooks. Standard air conditioning, Sentry Key® theft-deterrent system, easy access Fold-and-Tumble(TM) rear seat and a choice of Dark Slate Gray vinyl or cloth seating. Available in red, silver, blue and black exterior colors. Tomb Raider Edition Rubicon: 16-inch Alcoa forged aluminum wheels Tomb Raider badging with serial number Light bar Riveted fender flares in graphite Black Tubular grille guard Diamond plate bumper guard Rock rails Fog & Taillamp brush guards Aluminum diamond plate bumper guard in black Dark Slate fabric seats with red accent stitching down the center Silver surround instrument panel bezel Red seat belts Available in Bright Silver.
2002
New Exterior Colors: Shale Green Metallic New Ecco Wheel and Tire Group with P225/75R15 OWL Tire replaces the Grizzly Wheel and Tire Group New appearance for the Full Face Wheel 30″ Tire and Wheel Group, speed control, full doors with roll-up windows and sentry key are now standard on the Wrangler Sahara Full doors with roll-up windows, fog lamps and tow hooks are now standard on the Wrangler Sport Fog lamps and tow hooks become separate options New HVAC System with overall improvements in performance and quietness New Fuel Tank Skid Plate with Added Reinforcement Premium sound system that includes 2 new tweeters in addition to the existing subwoofer 7 year/70,000 Mile Warranty Offered (Not on early 2002′s however) Introduction of X Model: 4.0L engine and cloth seats, standard, less options than Sport (no Dana 44)
2001
New Exterior Colors: Sienna Pearl Coat Steel Blue Pearl Coat Amber Fire Pearl Coat Discontinued Exterior Colors: Medium Fern Green Desert Sand New 4-ply Soft Top that is more durable and quieter Quarter-Turn Fuel Filler Cap New Anti-Lock Brake System Long Life 100,000-Mile Engine Coolant that is more Environmentally-friendly Quick-Removal Side Steps All-New steering wheel tilt mechanism provides reduced effort and an increased range of adjustment Optional molded plastic Add-a-Trunk for reduced weight Optional Amplified Sub-woofer Re-designed Stereos Mini Console with dual cup holders Re-designed Full Console with rear seat cup holders Sutton Vinyl Seat Material – Standard on SE and Sport Nomad Cloth Seat Material – Optional on SE and Sport New wider inside rear-view mirror New Multi-function Steering Column switch combines headlamp, fog lamp, turn signal and windshield wiper functions Intermittent windshield wipers made standard New Instrument cluster includes a fog lamp tell-tale light and provides Parade-Mode lighting, battery saver control of interior lighting and odometer display with door open User-Ready Child Seat Anchorage System The pull switch for the headlights moved from the dash to the blinker Late Model: New Fuel Tank Skid Plate with Added Reinforcement 60th Anniversary Edition Available only in Black or Silverstone Metallic Body-color wheel flares and rocker sills Specially embroidered floor mats Full Metal Doors Canyon 30-inch Tire and Wheel Group Fog Lamp and Tow Hook Group Air Conditioning AM/FM stereo readio with CD player, five speakers and subwoofer Options: Speed control & Dual-Top
2000
New Exterior Colors: Solar Yellow Patriot Blue Pearlcoat Silver Stone Discontinued Exterior Colors: Chilli Pepper Red, Gunmetal Blue Intense Blue Deep Amethyst. Alternator moved higher up Ultra Star 16″ alloy wheel now standard on Sahara models. 4.0L engine now gets direct-ignition system (no distributor), re-designed cylinder head, new exhaust manifold and dual-catalyst system (2.25″ exhaust) New NVG-3550 manual transmission replaces the Aisin transmission on the models with the 4.0L engine (includes synchromesh on reverse gear). Sound Bar now standard on Sport models. Tow hook option now includes one rear tow hook. Sport’s standard AM/FM radio adds a cassette player, Sahara exchanges a cassette player for CD player. Optional tilt steering wheel in SE and Sport is now the same leather-covered unit that was standard in Sahara. Child-seat tethers added to the rear seat,
1999
New Exterior Colors: Medium Fern Green Pearlcoat Forest Green Pearlcoat Desert Sand Pearlcoat Intense Blue Pearlcoat Discontinued Exterior Colors: Jade Lapis Blue Emerald Moss Green Gunmetal Pearlcoat New Interior Colors: Agate Camel New Top Colors: Dark Tan replaces Spice. Hood cowl changed from a “3 section” wide cowl with alot of plastic around it to a smaller cowl… Removed annoying useless vent that leaks water Cruise control controls on steering wheel Rotary climate controls with bi-level air Defeat switch for passenger-side air bag Improved ECM Re-designed catalytic converter New “JTEC+” engine controller with new engine-function sensors Lighter frame – 16 lbs (8kg) lighter Nineteen gallon fuel tank now standard. 30″ tire package came with the “Canyon” style wheels (15×8).
1998
Chrylser becomes Daimler/Chrylser New Exterior Colors: Chili Pepper Red Pearlcoat Deep Amethyst Pearlcoat Smart Key Immobilizer replaces previous Lock/Unlock keyfob system. Cruise control Available Ez-Entry Driver’s seat now available Revised torsion bar for improved steering response Revised steering gear ratio that varies from 15:1 on centre to 13:1 at the extremes of travel for more responsive steering New steering wheel Next generation airbags Revised stereo range Hood latch changes 3.73 ratio rears and Dana 44 Rear New engine management system wiring Dual Tops Option Added pads to front bumper — front license plate moved to the center of the bumper 30″ tire package came with the “Gambler” style wheels (15×8) Changed hood vents from 3-wide to 1 in the middle Late Model: Defeat switch for passenger-side air bag
1997
Introduction of TJ Model: All-new, refined exterior body panels and hardware Quadra-Coil Suspension Contemporary interior appearance and dash New frame with outstanding torsional and bending stiffness Driver and passenger air bags Optional ABS Improved soft top (quieter and easier to put up/down) Round headlights return Lockable glovebox Available exterior colors: Black Bright Jade Satin Glow Citron Pearlcoat Dark Blue Pearlcoat Emerald Green Pearlcoat Flame Red Gunmetal Pearlcoat Lapis Blue Moss Green Pearlcoat Stone White AX-15 5-spd Transmission Annoying useless extra vent behind the hood that leaks water No screen to in cowl vent Cambolts for the front control arms Knock-outs for the rear control arm cam bolts Ability to display the diagnostic codes on odometer with key on,off,on,off,on You have to switch a plug to disable the clutch/starter interlock AX15 for the Manual Tranny or a Chrysler 999 for the auto if it is a 6 cylinder AX5 for the Manual Tranny or a Chrysler 904 for the auto if it is a 4 cylinder Optional dana 44 with 3.55′s gears Front License plate on the passenger side of the bumper. Late Models: 3.73 ratio gears and Dana 44 Rear available Hood latch changes Ez-Entry Driver’s seat now available