In my area the zillas are already very rare. Max you see on my local CL at one time is like 3 and right now only two both over $2500 and only in fair condition. 
There are pile of 85-86 complete rust buckets and roached out too quite cheap though I might add.
And the 87+ are actually not that common in my area im not sure why.   

Back east here the zillas are pretty rare.  I looked for almost a year before i settled on a low hour stocker. All the modded ones were garbage.  I had one guy drop his price to "only" 2500 AFTER I showed him the super loose flywheel and very badly worn crank pocket/ bearing.  Im damned lucky it didnt blow a motor on the test ride.  Air leakin like a mofo.

WV im going down to trade a guy my kx for his 250 Saturday and hes in WV...

I think 87 500 and 87 250 will be the rare ones, seems to be what most ppl want

What about the 85' and 86' models? If it weren't for them, there never would have been an 87'! I think the 85' model especially deserves some credit as well. It's funny nobody has mentioned the later years. Did those years have any major engineering changes?

I've got a really clean original 87' 500 except for a HPR motor and pipe. My question is wether to keep it original or update and customize it? It would be cool to have something original, but it would also be nice to update the shocks and breaks and add some custom parts, any thoughts?

Thats around 80 miles north of me. Had alot of good times in Fairmont.  College days! How far from Fairmont are you Dp

I think the quadracers and TRX250, and other vintage trikes and quads from the 80's will eventually be like the 60's muscle cars of ATV world. The 85 LT250 will always have some nostalgia being the very first race quad, and to this day still the lightest full sized race quad ever made. (At 293 lbs dry, it weighed exactly the same as the 3rd gen Honda ATC250R's, and was actually lighter than a Tri-Z!) The 87 LT250R will of course be special because it was the first 6 speed powervalved motor, and also the only year of the large reed 250 motor.

The Honda TRX250 will also be remembered because it became so popular among MX racers and became the basis for so many aftermarket parts. But I think the quadzilla will be the most haloed and most valuable ATV simply because it had the largest high performance two stroke engine ever put in an ATV, and had a powervalve and counter balancer to boot (making it a more desireable engine for an ATV than someone simply putting a CR500 engine in a TRX frame.) The suspension was way ahead of it's time, and for the size of the machine, it was incredibly light. Similar sized machines that were made later (think DS650) weigh almost 100 lbs more. It was simply the baddest ATV ever. Period.

There will never be another ATV with a motor that has the power to weight ratio that the zilla had as long as 2 strokes aren't produced anymore, or until some sort of mini Wankel engine is developed for ATV's. That fact is what already makes these machines legendary, and their value will go up as people realize this when they look back years from now and 2 strokes are a distant memory.

As for which year of the Zilla, I'm not sure. 87's were the first year, and had the larger reed cage which is sought after for those trying to make crazy power. However, they also had some issues that were corrected in later years (extra head stud, larger hub flywheels, better carb). I've also heard there were about as many '87's sold as the other three years combined which makes them a little less rare. (It sure seems that way when you see them for sale. My experience is about half of them that I see for sale are 87's)