I have class called Nod, hi have 3 dimension array
Short[][][] (better use 1 dimension ,but 3 dim better for debug)
Every nod have links to near Nods
Like
Nod Left
Nod Right,
Nod Top
You can hold them all not sorted in simple arraylist, same easy you can add new one
For render I use part of Nod (nod Quit big)
And create display list, why display ? test show display faster then VBO
Its quit simple get access to data in near nods, and + you have unlimited Y axis, not ZX like Minecraft
Cheers

Sorry don’t update own project, have managed rewrite my engine many time,
don’t have full gave for now(or part that’s can be played),
trying do Ai, also and 2D and 2.5(isometric)
http://imageshack.us/g/213/20120528200723.png/Also I decide that’s all games I relize will be fully free without payments, or stupid ads.
Maybe later add free donations, but not now

I really want do open source, but cant, its may produce to many not quality clones.
also slowly teaches pixel art use dune 2 like reference^^