Pretty much everything Super WARP released in the west.

Armored Core.

Dont worry the first one isnt canon or should i say its events take place in another dimension with other versions of the same characters, the series has improved a LOT from that first game, as i said the leap in quality from the first game to the second one is the biggest leap in quality i have ever seen.

That being said the game is still a niche tittle and therefore it doesnt have huge production values, for example there is very few cutscenes in the game and most (if not ALL) the dialogue is in a visual novel style, but the game isnt about great cutscenes or amazing graphics its all about the parodys to the gaming world (wether they are joking about consoles, games or events like the hack to PSN and the Kinect), the characters are also part of the appeal (with each of them representing a respective console), the combat is  quite solid, its turn based with free movement arround the field and with normal attacks that you can customize, special attacks that consume SP, EX attacks that are youre "ultra special moves" (mainly for killing bosses) and combination attacks that some character can perform toghether when they become closer friends through the lily rank (which is another game mechanic).

if you want to get into the series buy Neptunia Victory or any of the vita remake games, since this games have the most refined version of the combat and are really improved in comparission to the first entries of the series, or just wait for Victory II on PS4 that is bound to be the best one so far.

INTERESTING NOTE: inafune the father of megaman worked on this series and helped it become what it is today (a good Jrpg) and he is in the game as a special attack, its quite funny:

https://www.youtube.com/watch?v=KnxxdTZ79ZQ

https://www.youtube.com/watch?v=60UvsiuO-yY

Atelier series

would Tales be considered niche? if so thats another

Also playing Hyperdimension Neptunia for the first time and loving it =)

is harvest moon niche? that'd be my choice.

<--- Variable Geo.

Advanced V.G. 2 is one of my favorite PSX games, and probably the best one in the franchise. I like Super Variable Geo on SNES too.

Ar Tonelico
YS series

Well, if a niche game is targeted toward a specific audience...

I would go with Rune Factory and Harvest Moon

Combat Mission - WeGo turn-based military strategy franchise.

Shin Megami Tensei.

Though its popularity is growing, I still consider it niche.