Beyond Good & Evil - If you like the Zelda games than you will like this game. From the combat system to the puzzling to the story (The planet is called Hylis, change a bit and you get Hyrule) everything reminds of the Zelda games. It has a great ambience of discovery and yet familarity. The fighting system might not be the strongest selling point (Attack, hold attack to do a strong attack, block, dodge), but the atmosphere with a lovely soundtrack [http://www.youtube.com/watch?v=7qOGqHE2FS4] sure is. And the graphics; Well, they're PS2 graphics so don't expect too much. But they somehow fit in a strange way.
I'm not sure if it's really considered "lesser known", but when it came out, it was kind of missed by everyone but a few.
Now the indies:
World of Goo - It's often called a puzzle game. I rather see it as a journey in a strange and bizzare world. There's some puzzling, but it's always straightforward and rather a game of finding a balance of the gooey towers so they don't crumble.
Again, not sure if it's considered "lesser known"
A.R.E.S. - Megaman with different skins. But it's Megaman. That's even what the description should say: Megaman with drawn 2D sprites infront of a 3-Dimensional background made of drawn 2D sprites.
Trine - Interesting and challenging 2D action-puzzle-platformer. You have three characters that have each different abilites and your goal is to reach the end of the level:
The Mage - Can summon boxes and plates and levitates them around to build bridges or stack them to stairs. The Rogue - Can shoot enemies with her bow and a range of different elemental arrows. Can also use the grapple hook on any wooden surface to swing from place to place. The Warrior - Can smash enemies with the hammer or slice with the sword. Also has the shield to block attacks and falling debris and spikes and whatnot that tries to kill you. Also, has the most health and can smash rocks and such.
Now the tricky thing is that they're all trapped in the "Trine". That means you're only able to have one heroe activ at the time, but can change instantaneously with the push of a button.
There are a lot of places where you can outsmart the game or the level designers by being using more your platforming skills than puzzling, but that does not make it a bad game. The last level is incredibly hard in particular and I can't see how you're able to beat it without using all the tricks you can come up with.
Darwinia - Interesting to say the least. It's some sort of RTS but without any familiar RTS elements. It's really hard to describe what it actually is. It's like an RTS-Sim...
I think it's a really strange experience and differs from the usual "Send out collectors that collect materials, then build a barracks, then train soldiers, then send them to the enemy, once you have enough resources, build the armory, then you can build tanks". It has absolutly nothing of that. You have direct control of one squad of...anti-virus programms and shot enemy virii. At the same time, you need officers to direct the self-concious Darwinians to points and machines that they have to operate. But they have to be protected by the Squad since they're helpless on their own. You see a lot of virii clustered together? Send in the air support which sends a group of Space Invaders that drop bombs on them. You have to defend a position against virii attacks? Send in an APC that transforms a turret and man it with Darwinians.
Defcon - This is also quite a strange gem. It's the most accurate simulation of a nuclear war I've ever seen. At Defcon 5, actual nothing happens. You can make treaties or secret agreements if you're playing in multiplayer (which I guess is empty after 6 years).
Defcon 4, units are being placed. Radars, nuclear silos, fleets and nuclear submarines, airports with nuclear bombers and fighters are available. That's already the entire list.
Defcon 3, the battle and the hostile actions begine. The battleships shot each other, the fighters fight other fighters, nuclear subs are being hunted down, the enemies defences are being checked. Defcon 2, same as 3, but action intensifies. The nuclear war is about to break out. Bombers are being launched, the naval battles are being decided.
Defcon 1 - All hell is about to break lose. The authorisations for the ICBMs, MRBMs or SRBMs are being given. Everyone is getting incedibly suspicios of everyone else. "Should I keep my nuclear silos in defensive position to intercept enemy missiles, or should I change them to offensive to fire my missiles?", "Who is going to fire first?", "Who will shot me and when?", "Did I destroy all their subs? Are they maybe hiding somewhere infront of my coastline?", "Does the enemy know I've got subs station and ready to fire on him?".
And then, when you hear "Nuclear launch detected", the holocaust begins. This game is unbeatable. It's just horrific to watch a nuke pass your defenses and slowly moving towards that big white glowing dot that says "New York, 10 Million". You see it getting closer and closer and you can do nothing against it. It hits. A number pops up: "4.5 Million dead". All over your continent you see "3.3 Million Dead" here and "2.1 Million dead there". You let your submarines surface and unleash a barrage of nukes. "Moscow, 4.7 Million Dead", "St. Petersburg, 3.8 Million Dead".
Even thought it's graphics are basicly just pictographic shapes and numbers, I think this game is incredibly horrific. But, you need to be very patient. One round takes about 1 to 2 hours if speeded up. You can also play it real time. But then it really takes 30 minutes for a nuke to fly from America to China. There is also the ability to play with goals e.g. "have the most kills" or "have the least amount of casualties" or "get +2 points for a hit, loose -1 point if you're getting hit".