It feels weird that I can't put down Okami anymore.
Gaurdian's Crusade is a very obscure, very humorous RPG aimed at younger audiences. It can be enjoyed by anyone though, and has a very moving surrogate family thing going on with the three main characters. You get to raise a Baby Dragon monster, train it, spoil it, scold it, feed it and customize it's abilities. Depending on how kind you are, and how you balance that kindness with strictness, you can give it orders in battle or end up having it hate you and start attacking YOU in battle.
Also has a unique spin on the whole 'destined hero' trope. It plays with a lot of RPG stereotypes, and kind of takes the piss out of the Tales, Dragonquest and Final Fantasy stereotypes. Not in a hateful way, it just shows that there's always two-sides to every story in a very clever way. Pretty smart little story with some subtle comments on prejudice.
It's a fun little PS1 game, with lots of unique story and gameplay elements. Stylish jazz/funk soundtrack as well. Only flaw is the aged graphics. But good luck finding it. Very obscure, but I saw plenty on Ebay and Amazon when I recently bought my new copy.
Other than that one example, I have no idea. Everyone's mentioned the other ones I know. This really is an industry built on franchises. Mario, Zelda and Final Fantasy's influence in the 80's saw to that (for better or worse).