So, this thread is only about games that not many people played, games that are not as popular as your usual Zeldas, Marios, Metal Gears and Final Fantasies, games that are either not very good or just obscure but have soundtracks so good that can be compared with the best and most popular OSTs.
Goemon's Great Adventure (N64) is my pick:
https://www.youtube.com/watch?v=HNXn3xssdng&list=PL0D877BD1284957FB
This is just one of my favorite songs in this OST but please, give a listen to the rest of it. Make sure you have some free time though because this OST is HUGE, yet i don't remember many bad songs in it. The game itself is just a "decent" 2D-ish platformer. Not the best, not the worst. It exists. Definitely not the most popular N64 game, even among N64 fans, especially considering that the first Goemon was a better game.
But this OST is definitely one of the better i came across during that generation. Which is a shame really because due to the low popularity of the game, not many people listened to it.
As far as I remember many tracks are remixes/rearrangements of the first N64 Goemon game but I haven't listened to it as much, to be honest, so I might be wrong.
Mystical Ninja Starring Goemon's OST on the other hand is one of my all-time faves (the game itself, too). Just listened to it the other day
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Now onto my first pick: the "Enemy Zero" soundtrack, composed by Michael Nyman. Obscure Sega Saturn game by the late genius Kenji Eno ("D", "D2" and other very leftfield, creative games). Read this interesting piece from 1UP on his work!
Michael Nyman is a well-known, british movie composer of mostly minimalist music.
Check out these tracks and the others in the playlist:
Enemy Zero OST - Confusion
Enemy Zero OST - Aspects of Love
Enemy Zero OST - Laura's Dream
Second pick would be "Opoona" for the Wii. Very quirky, unique JRPG with a really good soundtrack from Hitoshi Sakimoto's music company Basiscape. On this specific soundtrack the composers were Hitoshi Sakimoto, Masaharu Iwata, Manabu Namiki, Noriyuki Kamikura, Kimihiro Abe and Mitsuhiro Kaneda.
Found the game for 5€ or something like that in a Gamestop in Berlin and was totally surprised by the music, though I only played a few hours. Immediately got the OST.
It has a lot of wonderful synth-heavy tracks with very playful arrangements and nice melodies.
Opoona OST - Space Ship (Hitoshi Sakimoto)
Opoona OST - At Tokione (Hitoshi Sakimoto)
Opoona OST - Matia Mine (Masaharu Iwata)
Opoona OST - Blue Desert Hotel (Masaharu Iwata)
Opoona OST - At Lifeborn (Manabu Namiki)
Opoona OST - Garden Of Arts (Manabu Namiki)
Opoona OST - Concert Hall (Noriyuki Kamikura)
Opoona OST - The Village Without Memories (Noriyuki Kamikura)
Opoona OST - Great Dunes (Kimihiro Abe)
Opoona OST - East Sea (Kimihiro Abe)
Opoona OST - Holy Island (Mitsuhiro Kaneda)
Opoona OST - A Walk In The Sea (Mitsuhiro Kaneda)
With my last pick I'm not sure if it counts as "obscure" but nevertheless: "Threads of Fate".
Only played it for a few hours but LOVED the soundtrack. I'm a big fan of Junya Nakano (th one on the left, next to Nobuo Uematsu and Masashi Hamauzu) who worked on FFX (examples: 1, 2, 3, 4, 5, 6), FFXIII, Tobal No. 1, Musashi: Samurai Legend, etc. He's a master of ambient and percussion-heavy tunes. The Threads of Fate OST might be his most melodic work.
Threads of Fate OST - Theme of Dew Prism
Threads of Fate OST - Passing Through the Forest (Man, I love this one so much!)
Threads of Fate OST - Rasdan
Threads of Fate OST - A Chance Meeting
Threads of Fate OST - Church
Threads of Fate OST - Village
Well, so far so good. I might post some other ones later
EDIT:
Tsugunai Atonement on the PS2 had some pretty bitchin music
https://www.youtube.com/watch?v=MVZ0M41le4I
Aaah, thanks, I knew I forgot one! Love this soundtrack, too! A lot of Chrono Cross-like tunes. I'm a huge fan of Yasunori Mitsuda.
Tsugunai: Atonement OST - Early Afternoon In The Village
Tsugunai: Atonement OST - Nabi Fairy
Tsugunai: Atonement OST - Fisela's Theme
Tsugunai: Atonement OST - The Devil Lol, just noticed it sounds a bit like Nier.
Napple Tale Vol. 1/2. Obscure Action-RPG on the Dreamcast with music composed by the absolutly amazing Yoko Kanno (Cowboy Bebop soundtrack!!!). This woman is unbelievable. I don't know any composer with such a quantity/quality ratio. I have 1517 songs from her on my hard drive and I only skip 2% of it (and only because I don't like songs with Japanese singers with too squeaky voices anymore). Even her "worst" tracks are still great.
Napple Tale Vol. 1 - Chocolate Forest
Napple Tale Vol. 1 - Snow Princess
Napple Tale Vol. 1 - Rain Waltz
Napple Tale Vol. 2 - Ball Jar
Napple Tale Vol. 2 - Rabbit Bed
Napple Tale Vol. 2 - Wild Wind