Not only do I personally consider the following game to be a hidden gem amongst adventures, but I also regard it as being a top tier Nintendo DS experience which went largely unnoticed by people. The development was actually quite progressive, thinking about it in hindsight. The game was created in Japan which is known for being conservative, and additionally it was released in 2008. Both of those factors make it fascinating that Time Hollow was in fact led by a woman. Junko Kawano was responsible for the scenario, game planning and original character design.

I first played it in the early 2010s, and loved nearly every second of it. Time Hollow makes excellent usage of the stylus pen in a way that feels relevant to the game's plot rather than being a gimmick. The soundtrack is crafted to perfection, fitting each situation accordingly and pleasant to listen to in general. Briefly I will be critical of the lack of adequate signposting with one of the earlier puzzles, I got a bit stuck there because of the control schemes, however, excluding that one-off example, it's easily a fantastic experience from beginning to end.

Now let's get to the remainder of the quality aspects this game offers: Visuals, friendship, gameplay mechanics and replay value.

The setting is a peaceful small town which walks that fine line between being quaint and modern. The idyllic town and characters are illustrated in an anime/manga style that exudes refinement. Peppered evenly throughout the game it contains nearly 7 minutes of professionally animated cutscenes, which is certainly an interesting technical feat for Nintendo DS hardware.

You play the game as a high school student named Ethan Kairos. Complete with loving parents, a cute cat, tight-knit group of friends, etc.

*looks at watch impatiently* I'm certain nothing will happen at all to change this situation within the first 5 minutes. 

Admittedly, the characters are somewhat stereotypical, but this is entirely forgivable as you end up caring for them anyway. This is a game that understands the importance of pacing by balancing the carefree moments with the dramatic at the correct intervals.

I love that they included optional sidequests alongside the mandatory plot progression tasks, this in turn affects the timeline which is a very cool element. A lot of the gameplay involves opening time rift portals to change things in the past to alter the present. Various inventory items play into this time mechanic as well. The game features a total of three different endings. The standard ending, plus two alternate endings.

With the development, publishing and financial backing of the colossal industry giant Konami, I would not have been surprised if they were trying to set Time Hollow up as the beginning of a new game series. Nevertheless, a sequel didn't ever come to fruition. Production value is something I respect in general. The team effort of 139 diligent workers resulted in a 7 hour amazingly condensed game, which I can confidently refer to as a sparkling hidden gem that is worthy of a new appreciative audience. 

https://www.mobygames.com/game/37777/time-hollow/

https://en.wikipedia.org/wiki/Time_Hollow

I have to mention "Keepsake" here. I totally ignored this one when it was released, and don't even know why. 20 years later, I bought it on Steam and I was amazed, I really liked this game. Wish it would be possible to get a remake or remaster for this.

I actually considered mentioning it in my list as well, so seconding this! (I was mainly just unsure how "hidden" it was.)

Originally played through it with a friend way back when, and replayed it again four years ago. I enjoyed it a lot, though it's a flawed gem for sure. Instead of repeating my own words, I'll copy my Steam review of it here:

"What if you arrived as a new student at Hogwarts, and all the teachers and students had completely disappeared?" That is very much what this game feels like when you play it.

Keepsake is a good story that could've been better told. I can't comment on other languages(since the game is available in multiple languages, including full voice acting), but the English voice acting isn't exactly great. In addition, there are definitely story elements that could've been told much better for greater effect.

That said, it's definitely a game worth playing through. There are some bugs and crashes, but there are lots of interesting puzzles, a really good hint system, and it does have a some unique traits.

The music is pretty good, and the visuals is that good, old prerendered 3D style, with some small video cutscenes now and then.

(The art of the main characters as children might give you nightmares, though! The artist has hopefully improved since.)