Here's a straight answer:
1987-1989 were J-arm frames. 1990+ were a-arms. This is a matter of personal preference, but as said before, aftermarket suspension for a-arms is much easier to come by. Throughout the years they changed some electrical plugs, tail light, frame and plastics colors, and rear shock. Other than that, nothing else has really changed.
Obviously, the newer the bike you buy, ODDS ARE the less it's been used. Of course that is not ALWAYS the case, but if you had a choice over a 1992 or a 2006 for the same price, I would choose the 2006.