An OST that probably nobody would mention, but is very dear to me, is this:
The composition here is something few would dare imagine making for such a humble piece of hardware. Luckily, by that time the Japanese had realized that game music could be much more than bleeps and bloops, and Kenji Ito did a true miracle with the very first Mana game. This OST is legendary to me, and I believe it inspired game musicians to do better with the GB hardware.
Megaman X has a ridiculously good soundtrack. The trifecta of Spark Mandrill, Storm Eagle and Armored Armadillo is top-tier video game rock, with Armadillo in particular having some of the strongest composition ever heard on the SNES.
Megaman 2 and 3, hard to choose one over the other. 2 is a legend, with Dr. Wily Stage 1 being possibly the best NES track ever written, but 3 is just as consistent and really brings the NES a step further.
Coming to Castlevania, we have CV3 that in its Japanese version has without a doubt the most amazing music ever heard on the hardware. Then you have Dracula X on the PC-Engine, with its godly early-90s CD rock. Lastly, of course, there's Symphony of the Night, a sumptuous game with an equally sumptuous soundtrack that's just crazy in its quality and variety.
Donkey Kong Country 1 & 2 are both outstanding, especially when you consider that they sound completely different than anything else on the SNES and in that generation altogether. I'd say 2 is the strongest, taking the already incredible quality of 1 several steps further and making everything sound more intense and "gamey".
Chrono Trigger, Chrono Cross and Xenogears. It's sad to admit that Yasunori Mitsuda blew the better part of his load in his early career, but the three games mentioned above all have some of the best music ever heard in games, ever. Chrono Trigger is insane when you think it was Mitsuda's first big work in the field, while Xenogears and Chrono Cross did stuff nobody had dared before, probably not even Uematsu.
Winds (aka Lords) of Thunder. The zenith of rock-metal game music. This soundtrack is as silly as it's brilliant, with its ridiculously exaggerated guitars and synths, but it's an absolute banger.
Nier / Nier Automata. Oh boy. These go a bit beyond words. There's literally nothing impossible anymore for game music since storage space allowed for the use of real instruments, but Nier's music is insane.
No list would be complete without Nobuo Uematsu's FF OSTs, and here it gets a bit hard to choose as there's so many. I'd say it's a toss-up between FF7 and 8, with an edge to 8 because of sheer sound quality, but 7 has so many stellar tracks you can forgive the rougher sound of it. FF6 is a bit less consistent in my opinion, but it does have some killer tracks, and Dancing Mad is easily the most ambitious piece of game music of its generation.
Nintendo deserves a spot here with Super Mario Galaxy. Not only the game is superb, but the soundtrack is unlike anything else Nintendo has done, and it's just fantastic through and through.
There's many other possible mentions, but I'm done for now.