The only name that comes to my mind as possibly good and made with an RPG maker is
Yume Nikki, and it's not really an RPG.
That said, I've never played it. I have a huge queue of indie games to play and it's somewhere late on it.
I have never played a game made with an RPG maker that I have liked, though. When the "free to use" graphics are used, it's a turn off. When the standard battle/movement system is used, it's a turn off. When they significantly mod the system, I think it would have been less work to just program it.
I too, would be interested in a good indie RPG to add to my indie queue, RPG maker or no.