Most of the stuff I liked in the 90's were bands that got started in the 80's and were still putting stuff out. I actually have some VHS of Liquid Television and 120 Minutes.
The Posies were a huge fixture for me in that era.
R.E.M. were still turning out great stuff along with Replacements (Westerberg) and The Ramones.
They Might Be Giants
Trip Shakespeare were awesome (later to become a more pop sounding Semisonic)
Sunny Day Real Estate
Jets To Brazil
Like someone else mentioned... Danzig. Even the new Misfits stuff was decent compared to some stuff in "The Noughties". Hahaha.
And of course the countless amounts of bands influenced by My Bloody Valentine's "Loveless" LP released in 1991.
And there was still a decent Punk scene with bands like Jawbreaker, Crimpshrine, Green Day, The Muffs etc..
The thing I liked most about the Grunge movement was that it opened up people's minds to different types of sounds and let some of the Alternative bands from the 80's get some exposure too.
I was just at The Haunt a couple of weeks ago to see Freezepop. Had an awesome time!