This is a little hard to answer because most people don't advertise the fact that they use Java. Minecraft is the obvious go-to answer.
Minecraft is NOT the go-to option in my opinion, it's just a bunch of blocks with some... meh textures.
In my opinion, polish and consistency are more important than realism.
You can still have a game with a 'simple' art style and say it has good graphics, because it's consistent.
Look at TF2 for example:
Sure, it isn't the most realistic thing in the world, but it's still incredibly polished and consistent.
I'm not a big fan of Minecraft's textures either, but they're still consistent enough to be called 'good' IMO. The overall polish of the GUI, items, particles and textures are what make it the go-to answer for this question.
Hell, even if something like VVVVVV or Love+ were written in Java I'd still say that they were the best looking Java games out there, just because of their consistency. I know I'm completely breaking away from the question here, but it doesn't have to be 3D to be considered 'good'.