90s are not really up there as my favorite decade of music but there's definitely still some great stuff. It was pretty easy to separate the cream of the crop, lots of my other favorite 90s stuff is generally only 1 fantastic album with the rest of the meat of the band coming in another decade (Poison the Well, MBV) or in other cases 1-2 album wonders (Botch, Zao) lacking the consistency of the other bands' outputs.
1) Megadeth
90s releases: Rust in Peace, Countdown to Extinction, Youthanasia, Cryptic Writings, Risk
This might be somewhat controversial, but the first half of 90s is easily the best era of Megadeth imo. Rust in Peace is arguably the best metal album of all time and the transition from thrash metal into a more traditional heavy metal style on Countdown to Extinction is very well executed. And then comes Youthanasia. The first truly "sellout album" where Mustaine proves that it can be done with grace and selling out doesn't necessarily mean that music quality has to drop. Cryptic Writings gets even more poppy and ends up being one of the most underrated Megadeth albums. Risk is Risk and we won't talk about it. Breadline is catchy and it's no longer the worst Megadeth album. Still not enough to bring the rest down.
2) No Doubt
90s releases: No Doubt, Beacon Street Collection, Tragic Kingdom
Tragic Kingdom by itself would have been enough to land No Doubt in this top 10 but the charm of their earlier albums shoots them up to #2.
3) Portishead
90s releases: Dummy, Portishead, Roseland NYC Live
How can you argue against pure brilliance? Thinking about it more, this should be #2 but I'm too lazy to rearrange the post at this point so meh. Roseland NYC Live might just be the best live album I have ever.
4) The Gathering
90s releases: Always... (who cares), Almost a Dance (who cares), Mandylion, Nighttime Birds, How to Measure a Planet
The 90s were a simple time, a time before The Gathering completed their transition from a doom metal based band into art rock and then into some synth stuff that was still awesome. Mandylion and HTMAP are the stepping stones of both directions, with Nighttime Birds merging the best of both worlds, being a pinnacle of The Gathering's discography, until Souvenirs at least. That said, every Anneke album is at the very worst a very strong 8/10 so you can't really go wrong with any of them.
5) Blind Guardian
90s releases: Tales From The Twilight World, Somewhere Far Beyond, Imaginations From the Other Side, Nightfall in Middle-Earth
In contrast, BG is a band that truly found its sound in the early 90s. Switching from blaring speed metal of the first 2 albums to the epic power metal sound they are most known for. Every album is brilliant.
6) Deströyer 666
90s releases: Unchain the Wolves, Six Songs With the Devil (EP), Violence Is the Prince of This World (EP), Satanic Speed Metal (EP)
Ok I know I said I wouldn't have bands with only 1 90s album on the list but sorry, Unchain the Wolves is just THAT good and D666 also released 3 great EPs in the decade. With their debut album, K.K. Warslut and friends declared "we are the kings of black/thrash" and then they never looked back (until 2009 but we can forgive that if a crappy album is preceded by the greatest 3-album stretch in history of music, right?).
7) Master's Hammer
90s releases: Rituál, Jilemnický Okultista, Šlágry
Two flawless cult classics, the pioneers of 2nd wave black metal are absolutely deserving of a spot on this list, even if Šlágry was a weird and unnecessary release.
8) Skyclad
90s releases: Wayward Sons of Mother Earth, A Burnt Offering for the Bone Idol, Jonah's Ark, Prince of the Poverty Line, The Silent Whales of Lunar Sea, Irrational Anthems, Oui Avant-Garde á Chance, The Answer Machine?, Vintage Whine
One of those bands that will never blow you away with a singular masterpiece record but every single album is great. I couldn't decide which one was the best if you put a gun to my head (I would probably go with The Answer Machine? but it wouldn't be 100% sincere). 90s were Skyclad's decade and neither Martin Walkyier nor the rest of the band have reached this kind of level ever since.
9) Sigh
90s releases: Scorn Defeat, Infidel Art, Ghastly Funeral Theatre (EP), Hail Horror Hail, Scenario IV: Dread Dreams
Another band that was trying to find their sound in this decade, though it's debatable whether they ever have or even tried to. 90s Sigh still fully embraced black metal as the basis of everything they've done and even though it was likely holding them back in a way, it results in a bunch of very charming records, ranging from the fairly traditional Scorn Defeat to the crazy and disjointed Scenario IV.
10) Converge
90s releases: Halo in a Haystack (who cares), Petitioning the Empty Sky, When Forever Comes Crashing
I had to fit one of the hardcore bands that I really enjoy in here and Converge won out. In the end, it's hard to argue against the sheer song quality on the 2 full-lengths they put out in the 90s. And no, the debut doesn't count.