Dwarf Fortress, as an example, has Armok Vision [0] that uses DFHack [1] which reads the data structures directly from the Dwarf Fortress process to provide an API layer to other tools and scripts. Armok Vision provides a 3D visualization to the 2D of Dwarf Fortress (in a separate process, by reading memory through Dfhack). It's pretty rad.

There's also the 2.5D "Text will be Text" plugin that actually alters how Dwarf Fortress renders tiles, stacking 2D planes so you can see more than 1 Z layer at a time [2].

[0] http://www.bay12forums.com/smf/index.php?topic=146473.660

[1] https://github.com/DFHack/dfhack

[2] https://github.com/mifki/df-twbt