It all depends on what you want to do with it.

For the 250:
85-86 is the lightest of them all, but requires the most work (like strengthening the frame, swingarm, and engine swap if you want more bolt-on go-fast parts)...fortunately a lot of the important parts are interchangeable or easily modified to accommodate from other years.
87 engine has the big reed intake, theoretically better for drags and hillshooting, uses a different piston than the 88-92, all engines from this year forward have powervalves and a 6 gear trans.
88-92 engine has the small reed, better for MX/trails, reeds are easier to find.
87-90 frame is the full-floater rear suspension, just like the 85-86, but with a stronger box-type bearing carrier for the swingarm, a-arms are slightly different and do not interchange with 85-86 years.
91-92 has a no-link suspension, heaviest of the frames (and supposedly strongest), and some came with nice graphics from the factory.

The best year for the 250 is truly personal preference, and the 87-92's all perform about the same, while the 85-86 engine is virtually bulletproof if maintained at mild power outputs.

For the 500's...
The 87 had different a-arms, big reed intake, 6 bolt head, and some other minor things as opposed to the 88-90.
88+ 500's had the small reed intake and a 7 bolt head.
As with the 250's, all 500's perform about the same...big reed or small isn't important until you're at drag racing power output, and even then some small reeds can put big reeds to shame.
Fortunately, the cylinders are interchangeable provided you have the associated components for them (cylinder head, piston, reeds, intake boot, etc.), and that goes for all of the powervalved 250's as well.

KyleT is a member here who's done extensive research on the subject and can tell you if they used a different grade bolt on the fender mounts between year models if you're interested in that info.


Now, a hybrid is a completely different ball game, as you're retrofitting a 500 engine into a 250 frame (or maybe you want to go with something exotic, like a 500 powered Z400?).
You lose weight by utilizing the lighter frame and thus a hybrid will be faster than an identically powered zilla.
You will need some welding and fabbing skills, along with a hybrid pipe and some of the associated 500 components to bolt on your 250 frame.
Again, which year model 250 frame would be ideal for the conversion is also a personal preference...you want a lot of work, a strong frame, or a quick and easy project?
Big or small reed...again personal preference!
Sourcing parts is also a concern, are you going to pass on a big reed that's within your budget just so you can wait for months until a small reed shows up in your price range?
Would you rather use the frame you currently own, or find a frame that's better suited for you?


TL;DR
They're all about the same, they all have their redeeming qualities, find one that suits you personally because there isn't really a top dog here.