One of my favorite apps using the Merge Cube is Dig!
Using the app changes a simple cube with a bunch of symbols looking like hieroglyphics into another world. You can build and deconstruct the cube that looks almost exactly like Minecraft. The reason I like this app the most is that students can build using the app.
My students at the beginning of the year struggle with this concept of orthographic projection and being able to correctly sketch the block layout. Having students use the Merge Cube students can grasp that conceptual understanding that they don't get from a sketch. Last year I borrowed some of the wooden blocks our construction teacher uses and it was a great way for some of the students to see the finished product. The app allows students to see around each object looking at it from the sides and from the top.
What I would like to see is have students create their own and have stations at each group where students correctly draw the orthographic projection of their groups creation.
TIP: If you can't get a Merge Cube for each student, there is a shortcut. I printed a picture of one side of the Merge Cube and you can't rotate it like a Merge Cube showing each side, but students can use that one side to create especially using the Dig! app.