The 90's were banner years of ball-bearing hubs that spun to eternity. I can't remember a lot of wheelsets from the era that stood out, just the hubs and the unique wheels.

Dura Ace, from 7400 through today, spins like silk and you can't really go very wrong with any of those hubs (and you can still get them in ball bearing).
Campangolo's 90's offerings were almost as smooth, and certainly way up there in quality, especially their proprietary (but heavy) wheelsets.
Even the lower-tier ball-bearing hubsets were very good, and Miche made some very nice ball-bearing hubs to compete with Campagnolo.

At the end of the 90's, the "newer" factory-made sealed bearing hubs were starting to show up, and were not yet equal, in my opinion, to the good ball bearing hubsets offered. I'm not sure they were even the equal of some of the nice sealed bearing hubs from the 80's, like Suzue, Sunshine, and Suntour. They were, however, significantly lighter, in many cases. I've never considered it that much of an issue, but some do, when it comes to weight.

Rims were not much different from the 80's, when Araya and many others competed to get to the 300g/rim zone, limited pretty much by the need for braking surfaces.

On the consumer end, Mavic was doing a lot of the groundbreaking. HED was adding fairings to go aero, and Velocity was coming in hard. Early carbons like Spinergy's Rev-X were still using Shimano 6400 freehubs and ball bearings. Many "tired" wheels from now were new then, and you can really make a difference on a 90's bike with a modern wheelset. If you want to be period-correct, you'll probably get smoother, longer-lasting wheels, but they will be a bit heavier.

For me, the 90's were aluminum bikes with wheelsets like 105/Mavic CXP-whatever's, and not anything to get excited about. Heck, my 1995 Trek OCLV 5500 had 6400 hubs laced to Matrix ISO-II's. This was a wheel little changed from the late 80's, but a bit lighter rim.