Zoids Legacy for the GBA is another one of those rare gems that's not widely known. It features a story line that combines those of the different Zoids anime series into one. It has a lot of characters and Zoid machines to choose from which can also be customized and equipped with different weapons as well as other equipment. There's a lot of interesting tournament style battles some of which have different restrictions and requirements. It's a very fun game to play overall, with good music and graphics. The only downside unfortunately is that the actual translation itself is not best. It's still better than that of Breath of Fire II was on the SNES, but it could definitely use some script polishing.https://en.wikipedia.org/wiki/Zoids_Saga
Shogo: Mobile Armor Division for the PC also deserves more credit than it's given. Up to this day, I still think that it's the best FPS out there and I don't even like these types of games. Shogo is the only one that I was ever able to get into as an RPG gamer. Featuring anime style graphics, great music and levels, along with two modes of play: on foot and in a giant mecha robot, what's not to love? It's way better than all the other FPS games out there. And yes, I've tried the so called "popular" ones and didn't like them in the least bit.https://www.youtube.com/watch?v=cVPyJuK2daMhttps://en.wikipedia.org/wiki/Shogo:_Mobile_Armor_Division
And last, but certainly not least, the Gothic and Risen series also for the PC (and a few consoles as well) is a wonderful, but horribly underrated and overlooked series. They're both amazing open world series of games that were made well before Skyrim (which took many elements from them) yet are not half as well known in the gaming world. There's also different factions, classes, equipment, spells, quests and options to choose from. It's honestly a shame how many great German and Japanese titles go unnoticed in the U.S.https://en.wikipedia.org/wiki/Gothic_(series)https://en.wikipedia.org/wiki/Risen_(series)
Edit: I might as well mention Robopon 2 and Medabots, both for the GBA:https://en.wikipedia.org/wiki/Robopon_2_Ring_and_Cross_Versionshttps://en.wikipedia.org/wiki/Medabots_(video_game)
Both games are great and often overlooked. They both feature interesting 3 on 3 turn based battles with lots of different customization options for the robots used by the player. And by the way, Robopon 2 is much better than the first one was. It kind of reminds me of Robotrek/Slapstick for the SNES mixed with a bit of Pokémon.
Ys V and Brain Lord for the SNES are also often overlooked. The worlds are nicely detailed and the fast paced hack and slash battle system is definitely a welcome addition in a time where most RPGs were turn based. Brain Lord also has a lot of puzzles which are well designed. Sadly, this game is often overshadowed by The Legend of Zelda - A link to the Past. Whereas, Ys V is great all across the board. It's a bit short compared to most RPGs (requiring about only eight hours to complete). Other than that though, everything else about it (the graphics, music and storyline) is perfect. The alchemy/magic combination system was also very unique.https://en.wikipedia.org/wiki/Ys_V:_Lost_Kefin,_Kingdom_of_Sandhttps://en.wikipedia.org/wiki/Brain_Lord