There are always games you play and really enjoy, and then ask people if they know it... and no one ever does. Games like this are usually pushed to the back by more popular games, and are hard to get your hands on. Some games I'd consider hidden gems are.. Epic Micky, (Wii) Okami / Okamiden (Wii / DS) Spore ( Hero & that really hard DS one) (Wii / DS ) These games are all incredible and need more recognition! Any hidden gems you'd like to share?
Bahamut Lagoon comes to mind, although I'm not sure if it really counts since it was never officially released outside of Japan (to my knowledge). However a quality fan-translated ROM has been around for quite a long time now and I highly recommend it to anybody who likes tactical RPGs with playstyles like say, Ogre Battle.
Orcs and Elves is my first thought. Lost Kingdoms is my next. Rune Factory comes to mind, though it isn't that obscure.
Two that I will ALWAYS point to are Risk of Rain and Hyper Light Drifter. These are two really neat indie games with amazing pixel graphics and gameplay but I've heard little from other people about these games, and usually when I mention them people's first response is usually "... What?" Another that comes to mind is Gunpoint. Oh my word is that a fun game. The graphics and dialogue are amazing and the gameplay is such an awesome rendition of stealth-espionage in a 2D style. Honestly these are games I could not recommend enough to other people out there, everyone should play them at least once!
Hotel Dusk Room 215 comes to mind for me. It's an amazing Visual Novel/Puzzle game that features Kyle Hyde, an ex-detective, and his adventures in Hotel Dusk which all take place in a single night. It has an amazing story and has super creative and fun puzzles.