Cowboy Bebop (though that seems like a cop-out given how incredibly well the series has aged), the original Trigun, Excel Saga (half '90's, so I guess it counts?), the Ghost in the Shell movie, Outlaw Star (which, yes, pales in comparison with Cowboy Bebop, but has its moments).
Ranma 1/2 is mostly 90's, and if you can stomach the complete lack of overall plot, it's a nice bit of fluff.
I would include the first 24 episodes of Eva, but the last two completely ruin the series (fight me), and no amount of retconning with movies makes up for that (also fight me).
Also, La Blue Girl, if you want to go that route.