Admittedly I love ALL Harleys but these are what I think are their best ideas and innovations over the years!
They are in no particular order but these all came to mind when I thought of what the best 50 Harleys were in my opinion!

1983 XLX Sportster 
1987 FXLR
1988 FLST Heritage Softail
1991 FXSTS Springer Softail
1990 FLSTF FatBoy, the original
1978 FX Lowrider
1957 XL Sportster
2007 FXDB/i Street Bob Dyna Bobber and a great platform to customize!
2012 FLD Switchback it's a Dyna it's an FL, best of both worlds!
2007 Night Train
2011 XL883N Iron
1939 EL Knucklehead when they finally designed rockerbox covers to keep the rider from being completely bathed in oil!
1966 FL the introduction of the Shovelhead
2005 FXDWG Wide Glide (The last of the dove tails)
1984 FXST (they had kickstarts on those Evos!)
1984 FXWG (more Evo kickstarter bikes)
1991 XL 1200, the year that launch the 5 speed transmission!
2006 VRSCR Street Rod VROD (mid controls better suspension)
1994 FLTH Road King another bike that launched a subculture of Bagger Nation!
1983 XR1000 Sportster! Great engine design!
1958 FL Duo Glide... wow, rear shocks to go with my front shocks? What a concept!
1991 FXDB Dyna "Sturgis" model with the Belt Drive that replaced the chain forever on ALL Harley factory models
2006 Dyna Street Bob with the introduction of the 6 speed Cruise Drive transmisison (though 1st and 5th gear were still spur cut gears still made it one of their smoothest designs for transmissions for the MoCo ever)
2010 XL Forty Eight it's a bobber sportster with a big fat front wheel!
1969 XL Sportster, last of the kickstarts
2004 XL models (new rubber mounted suspesion)
1957 FL Panheads with the 'H' cam (many owners claim the H stood for Hotrod since it really gave a boost of power to an old design)
1943 to 1945 WLA (interesting fact: The U.S. Army still has the ability to produce 60,000 more of these bikes as they kept everything that Harley Davidson sold them back then.)
1994 FLHTUC the first Ultra Bagger!
2006 FLHX/i Street Glide the trim bagger. (they had an FLHX in 1984 and it was one of the last of the Shovelheads and came with a tour pak)
1994 FLSTN the Nostalgia (the newer version of the FLSTN is called the Delux... dunno what's so delux about it, no saddle bags!!!)
2005 FLSTSC Heritage Springer Classic (they have earlier versions but man all that fringe and the colors were hideous)
1996 FLTR Road Glide the Shark Attack!
1995 FXDX Super Glide Sport it is mysterious very popular!
1980 FXWG The Wide Glide with the flame tank, dove tail rear fender and Kick Start!
1976 Nova Prototype the Harley that never was! The Harley V-4 Experiment (coulda been fun give those Magna's a run for their money)
2011 FXS Blackline a throw back to the slim rear wheel softail design along with some nifty new designs over the rest of the bike.
2000 FXSTD Softail, sounds like an STD with that lettering but really a DIFFERENT ride that was wildly popular in the new century but soon scrapped and all the parts used on those hideous Rockers.
1983 FXRS Dual disk front brakes BAYBEE!!! 
2000 FXST Softail Standard the perfect platform for total customization!
2001 FXDXT the Super Glide T-Sport not only did it have bags and a windshield it had a cool fairing!
1970 FX "Boat Tail" which I honestly believe was inspired by Evel Knievel!
1999 FXR2 the first of the CVO bikes before the CVO division was created! Great bike with all the upgraded components and transmission!
1994 FXLR the last of the FXR's until the FXR2,3 and 4
1970 - * XR750 Flat Tracker! LOUD LOUD LOUD but COOL COOL COOL!!!
1936 1/2 EL Knucklehead... halfway through 1936 they had to re-enforce the frames with stress point structures because the original frames were buckling under the stress of the new 74" motor.
1981 FLT one of my personal favorite Shovel Baggers! Finally some good tin on it!
1948 S Model AKA the Hummer! Cool little single cyliner but had that Harley Appeal!
1972 XR750 TT another fun race experiment for Harley Davidson that spawned the Crotch Rocket look! And you thought the imports created that designe? Harley came up with it all first!
2006 VRSCD Night Rod just a damn cool VROD model!
2001 FLHRC Road King Classic, definitely a kick back to the old styling but classy look!

1948 WL didn't make the cut! I'm crying inside

Sorry man, they were great bikes in their own right but side valve motors were a dime a dozen and weren't very well looked after... BUT, you can rebuild almost any of them and make any one of them run like a champ with a new set of points a flat blade screw driver!:-)

Besides the caption I could write would just suck, for example: 1948 WL, well if you're not in a hurry and you plan on avoiding highways with a minimum speed limit of 45 and just stick to the side roads, this is the bike for you!(I know, I'm a smarmy prick!)

Well dang the only bike I had/ have that made the list was my old 69XLCH... and it made the list for the reason I hated the bike...

It made the list because it was the last of the Sporty kickstarters:-)

It made the list because it was the last of the Sporty kickstarters:-)

Yep and both are reasons I dis liked it...Kick start and sporty... Was running with 120 CI and just was not enough...;D

Black... was Bitchy first bike... 12:1 compression on fresh motor...Magneto, and kick only... Bitchy didnt have enough a$$ to kick! Luckily we lived on a steep hill.... She'd fill up the gas by can... coast down the hill...drop clutch and lite her up... knew she'd be back before tank was dry and wasn't hangin at any bars ;~).... Now about the '47...LAST of the Knucks...

Good post
1971 Super Glide one of my favs,they had that cool looking red white n blue model.I believe it was shovelhead motr too? anyway a lot of guys coming back from Nam would chop teh crap out of those babys, I guess the "super" glide was harleys early answer to tht trend?

That is a GREAT story. And having met Bitchy, yeah, she is a tiny little thing to be kickin over a 12:1 compression motor.

Only happens once in the couple of years I had her... Was wore out when I finally got her going... Kick button is my favorite invention, lol..

Old Sportsters these days pretty much should be upgraded to an electronic ignition module!

@wooly all those Knuckles make for some great retro rides and I guess when the Panhead came out they just sharply forgot about the Knuck for a few years because at the time they were just the greatest thing Harley had offered the riding public. Only to re-emerge later as the best looking chop jobs. But consider the Knuck era as Harley did at the time with the frame designs and lack of suspension the only innovation that came from that era was it was their biggest displacement and the advent of the rockerbox covers! 12:1 compression, did it have to be pop started in 4th gear? LOL:-)
@Bitchy Kickbuttons, I like that! LOL
@Bitchy

Also as a matter of fact, the Pans came out with a pretty fat price tag for the time but they had plenty of people buying them up until 1957 when you could buy a 1957 Bel Air for the same price as a 1957 Pan even with the H cam, $300!!! Both of which in almost any condition will sell today for over 300% of their original price tags!

Nice to see my old ironhead made numero ono mate..Yup back in 83 my old shitbox was pride of the fleet..Just like any old girl who was prime in 83 she's had a make over or 5 in her life time..Now she will be passed on down the line for the next generation to make into a cool old scoot for him...The meat chicken will have his own personal style when he finally makes it..CHEERS BOOF

BOOF what are you riding to Sturgis?

Hire bikes mate....Too bloody expensive to freight my bikes over there and back..CHEERS BOOF

Can I say 48 knuckle, I don't know why but I just think the knuckle is one of harley's best motors along with the evo. and that would be a 99 "street weeper" or Heritage springer . I know some of you think they are but ugly, but man as they gracefully make the arch of the turn all that frindge just sweeps the street, I think it is a sexy bike man, have a great one! "T"

The Knuckle was not produced in 1948 it was replaced by the pan head... doesn't mean they didn't still put them together but the motor changed in 48 to the Pan. FYI:-)