Some (most) aren't that popular (some due age and others due the company killing the game themselves) but i'll bring them up anyways.
Shin Sangoku Musou Online Z (With the capacity to modificate files nowdays, people now have the option to change the textures or even the models of the characters and given that Dynasty Warrior has a list of crossovers, it'll mean that people could probably make DWO but with LoZ or FE themes.)
C21
GetAmped 2
Cosmic Break
Cosmic Break 2
Onigiri (All from the same company which... kind of killed the popularity of the games themselves, the first four have some sort of build-in customization for textures and at least 3 for polygons, 2 have some sort of also build-in map maker as well and 3 of 5 are fairly old, all of them have Java as engine)
Creativere (Online Minecraft clone from Steam... F2P Online Minecraft Clone.. 'nuff said)
Mabinogo (People from AURA project had great breakthroughs on taking, using and modifying files from the original source, they are open source, there's no private server at the moment but someone's working on it, so if you want you could take it as a side-project but i'm not gonna have faith in only one person working on this, Nexon is killing the game)
Trove (Minecraft+RPG, fanbase hate the game yet they can't help but play)
Spiral Knights (Old game, dropped by Sega and Three Rings and saved by Gray Heavens, runs on Java, not that popular but that's mostly because lack of updates since long ago thanks to Sega's management)
Possible ones:
SkySaga (It'll be intresting to have a PS about a game that hasn't an official release yet)