Hard to settle on just one. In no order:

• ChuChu Rocket (Dreamcast): insanely fun and manic couch multiplayer game
• A10 Tank Killer II: Silent Thunder (PC): the soundtrack alone justifies the time to play this aging flight sim
• Virtual On (Arcade): this was ported to Saturn and the port is good, but the giant arcade machine is where it's really at with dual twin stick cockpits
• Mario Paint (SNES): Really fun non-game from a time when non-games were uncommon on home consoles. I have hundreds of hours into this
• Dungeon Keeper (PC): darkly comedic evil dungeon lord management sim. I will never forgive EA for what they did to Bullfrog and subsequently the DK franchise. There have been many attempted homages and clones but none have captured the magic.
• Super Tennis (SNES): an actually fun tennis game
• Super Play Action Football (SNES): football game with a unique isometric view
• Hank Parker's Super Black Bass 2 (SNES): super fun fishing sim. I wish there were games like this today that took fishing more seriously and less arcadey.
• Brain Age (DS): a genuine sensation in its heyday and largely forgotten now. Really showed off the potential of the DS
• Cel Damage (GameCube): twisted metal with zany little cel shaded cartoon characters. Never got the respect it deserved and probably never will since they butchered the game's balance with the HD re-release

Any love for the Monkey Island series here?

Planetside 2 - someone else already mentioned it here, but it's the only game in it's genre and nothing else really comes close to what it offers (persistent 1v1v1 +300 player battles across infantry, land, air, and sea). It's been kicking for over a decade now and I'm not sure what could replace it if or when it finally kicks it. It's truly singular, and responsible for some of my fondest memories in gaming. It's also free!

Mine is Dark Cloud. It was a PS2 launch title (or near enough to it) that was sort of a PlayStation answer to the Zelda franchise. Along with the original Spyro trilogy, Dark Cloud was by far my most-played game back in the day. It had an absolute banger of a soundtrack and a few pieces of really interesting unique gameplay including an RPG element where the primary progression system was not in your characters, but in upgrading your weapons, and a city-builder where you have to place all the people in each village near or away from various other elements in the village to meet their needs.

I almost never hear anyone talking about Dark Cloud, but extremely randomly one of the like four Twitch streamers I actually watch (all of whom are Age of Empires streamers, because that's basically all I watch these days) happens to play its soundtrack frequently on her stream as background music. So that's been really fun.

I never see anyone talk about Ni No Kuni: Wrath of the White Witch but it's one of my favorite games of all time. The Studio Ghibli collab makes it ooze charm.

Let's see what I can come up with (and see if I can remember the names correctly!):

• NES: Back in the day, it was probably River City Ransom. Growing up, it was a game my brother and I loved to play... but no one ever knew what we were talking about at the time. Now the Kunio games are a bit more known, and with River City Girls 1/2 they're getting attention, which is great.
• Gameboy: Avenging Spirits. When I was younger, a friend and I loaned each other a bunch of our games. Sadly, he ended up moving away before we managed to swap back, and he got the better end of the deal when it came to the games. However, I did get left with a copy of Avenging Spirits... the game is a bit strange but its very fun and the sprite work is just adorable.
• SNES: Dragon View. It has great sprite work and a very (at the time) cool looking 3D overworld you can stumble around in... Solid gameplay and some RPG elements make it a nice little gem of a game.
• GBA: River City Ransom EX. Same deal as the NES version. I worked at Toys R Us around this time, and I think I'm the only person who purchased this game from the store...
• PS1: Brave Fencer Musashi. Someone else already mentioned Einhander, so I'll go with my other go-to PS1 gem from Squaresoft.
• Saturn: Guardian Heroes. While I bought the console for X-men vs Street Fighter, I go it with a handful of games on the cheap at EB Games: Magic Knight Rayearth, some crappy 2D Dragon Ball Z game, X-men vs Street Fighter (and a 4in1 cart of course!) and Guardian Heroes. Its such a well made beat-em-up that really doesn't get a lot of love because most folks never played any Saturn games.
• PS2: Way of the Samurai. Maybe not super unknown, but definitely a niche game back when it released in the US I think.
• Dreamcast: Cannon Spike. I bought my DC for Capcom games (and SoulCalibur), and this is one of the many gems on that console that never really pops up in discussions. I bought it on the sole merit that Charlie/Nash was in it, but it was wacky and engaging enough to warrant a place in my heart.
• XB360: Tenchu Z. I loved Tenchu back on the PS1/PS2, but this was probably the one that most folks didn't touch... it was a bit weird but a friend and I played the hell out of it on many a weekend back in the day.

Any other console I either didn't own (Genesis, Gamegear, PS3, etc) or just couldn't think of anything that really stood out as a hidden gem (PSP, PSV) or are more current and also don't really have anything that ranks (PS4, PS5).

Golden Sun. They were the best RPG games I've ever played and never get the love they deserve. Don't know why, I've never played a game that struck me like those 2 games did.

The first few Advance Wars games too, Advance Wars and Golden Sun were a huge part of my childhood.

N+ it's such a good game and no one ever knows what I'm talking about.

Loco-Roco for the PSP. As a game developer, I consider this to be the pinnacle of game development. It is completely original, uses only two buttons, super intuitive, yet your drawn into it and want to play for hours. It makes me sad that few have heard of it.

Toy Story on the sega genesis (and snes) is a close second. It is actually a bit of a hot mess, each level is a completely different style of gameplay. But it is super rewarding to fight your way through to the end. And it showcases so many different styles of gameplay.

Favorite obscure game?
Panther for Commodore 64 - The music is awesome!

Rez for Dreamcast/PS2 - not everyone talks about this game but the audience is a lot larger now than it was back when it came out for the Dreamcast and PS2 now that Rez Infinite is available in almost every current platform including the PSVR2.

I would’ve also said Another World (aka Out of this World) for the PC and SNES. But this game is also not-too-obscure like Rez. There are articles about it & the creation, re-released in almost every platform including the PS Vita, spiritual successors, copycats, and so on.

Star Wars Republic Commando! Every now and then people talk about it, but it is a shame it isn't mentioned more. I actually just replayed it, I'd almost say it holds up today with the remaster mod and the rc patch. There is also a very cool mod called "slightly remastered" which adds stuff like 3rd person scripted animations and scripted kill cams, it makes you feel like a badass! Aside from that, I'm also surprised nobody in the boomer shooter enjoyer crowd talks about Cube 2: Sauerbraten, which is a very fast paced arena shooter. The only server that is consistently active uses one shot rifles that have enough recoil to do trick jumps, very fun to hop on for a few hours

Rise of Nations. It's like Civilization but as a real-time strategy game and I really enjoy it. Microsoft actually released an updated edition in 2014 which was good of them but I basically never hear anyone actually talk about it which sucks because it's such a cool game. The single-player Conquer the World campaigns are also cool, and have some elements reminiscent of the classic Risk board game.

There's also Star Trek: Bridge Commander, which is often mentioned in discussions of "what Star Trek games were good?" but not much outside of that context. It strikes a perfect balance between having starship combat that really feels like you're commanding a ship with a lot of mass behind it and actually being fun and easy for an average person to pick up and play (which is where stuff like the X Universe games fall down). There are tons of "space fighter" games out there but I've never really seen anything that captures space capital ship combat as well as Bridge Commander.

Warzone 2100. A seminal classic for me, from the year 2000.

Power Blade on the NES. You are a Schwarzenegger-in-his-prime-like character in the future fighting the robotic underlings of an AI gone rogue. It has only 7 levels or so, but it has a nice gameplay to it, and the music was composed by Kinuyo Yamashita, who also did the Castlevania music. Needless to say, the soundtrack is top notch.

Rebel Galaxy Outlaw. Made by I think 3 or 4 people. Solid space flight shooter with charm. It's just fun.

Is anyone familiar with American Conquest? That game was excellent! The soundtrack is still stuck in my head.

I don't see anyone talking about CrossCode, but it's such an amazing game. And it's on sale right now!

https://store.steampowered.com/app/368340/CrossCode/

Profound story, excellent sound design, amazing soundtrack, insanely well designed combat system. It's just an incredible game. It has more content, depth, and attention to detail than most AAA games these days.

If you're picking it up, get the DLC as well! It's not just DLC, it's the conclusion of the game's story!

Crusader No Remorse, Crusader No Regret and Civil War Generals 2