Lots of gems from that era. In addition to the ones already listed, here is what I have in my collection which fits your parameters (prog, or can reasonably be considered "prog", from 1991-1997):
Abraxas - Tomorrow's World
Abstrakt Algebra - s/t
Alias - Metal to Infinity
Amorphis - Tales from the Thousand Lakes
Arkhe - s/t
Confessor - Condemned
Decoryah - Wisdom Floats
Decoryah - Fall-Dark Waters
Digital Ruin - Dwelling in the Out
Dominion - Interface
Dominion - Blackout
Dreamlore - Confined to Destiny
Eternity X - Zodiac
Eternity X - Mind Games
Eternity X - The Edge
Exises - Reternity
The Experience - Insight
Fifth Reason - Psychotic
Forever Times - s/t
Gone - Weakness Within Living Memory
Heaven's Cry - Food For Thought Substitute
Ivanhoe - Symbols of Time
Ivanhoe - Visions... and Reality
Letter X - Time of the Gathering
Letter X - Reflections
Leviathan - Deepest Secrets Beneath
Leviathan - Riddles, Questions, Poetry and Outrage
Leviathan - Scoring the Chapters
Lion's Share - s/t
Lion's Share - Two
Lord Bane - Age of Elegance
Mayadome - Paranormal Activity
Megace - Human Errors
Memory Garden - Forever EP
Memory Garden - Tides
Mercury Rising - Upon Deaf Ears
Opeth - Morningrise
Opeth - Orchid
Opposite Earth - Headspace
Psyco Drama - The Illusion
The Quiet Room - Introspect
Reading Zero - The Actual
Royal Hunt - Clown in the Mirror
Sea of Dreams - Land of Flames
Seven Signs - Silence of a Wish
Sigh - Hail Horror Hail
Tad Morose - Leaving the Past Behind
Tad Morose - Sender of Thoughts
Tad Morose - Paradigma EP
Tad Morose - A Mended Rhyme
Thought Industry - Mods Carve the Pig: Assassins, Toads, and God's Flesh
Thought Industry - Outer Space is Just a Martini Away
Tiles - s/t
Tiles - Fence the Clear
Treasure Land - Questions
Twilight - Eye For and Eye
Veni Domine - Fall Babylon Fall
Veni Domine - Material Sanctuary
Veni Domine - Spiritual Wasteland
Wicked Maraya - Cycles
X Factor X - s/t
EDIT: I've just realized that about 80% or so of my prog collection comes from the 90s. I guess the newer stuff doesn't do it for me as much.