This probably does not qualify as "popular game", but talking about Java games I'd like to mention Terasology (https://github.com/MovingBlocks/Terasology). It's an open source voxel game (Minecraft-like) and the LWJGL-based graphics engine looks very impressive to me (some screenshots here: http://terasology.org/gallery.html).
Might be AXIOM from the Apertus project: https://www.apertus.org/axiom