From the FAQ:
From 1986 to 1993, the only change was an inch rise added to the handlebars from 1987 on. In 1994 the front brakes went from single to dual piston calipers. The new forks, from the ZR1100 Zephyr, went from air to mechanical preload and lost their oil drains. A wider 5 spoke front wheel was added with a new rear wheel restyled to match. The dash cowl was redesigned, the instrument panel is from the ZX11, and storage pockets were restyled with locking lids. Adjustable hand levers also came from the ZX11. A new zoomy front fender was added, along with a stepped Corbin style seat (early and late seats are interchangeable). In 99 the forks sprouted little stone shields. That's it for changes. That's why the yearly color used to be such a hot topic.
Note:
The entire front fork & wheel assemblies will swap between the early models ('86-'93) and the late models ('94-'06), but you can't mix the parts. For example: early fork, late wheel.