Edit 2016-03:
3D-Maze game models designed to be capped with transpatent acrylic sheets at top and bottom.

I finally added the source-code with which I generated those mazes.
This was ~5 years overdue!! Sorry for the "slight" delay.
The code is a rather horrible hack - but I checked and it still works.
(The code is public domain) To use it load the haskell source file in ghci (the interactive haskell interpreter) and type "help". To adjust maze size / labyrinthicality / inhomogenity / ... you need to change the source-code since all that stuff is hard-coded.

If you want to do elegant idiomatic maze generation in in purely functional programming style (which surprisingly is possible although the problem at first sight seems to require destructive updates) I highly suggest you look at Tikhon Jelvis' work:
http://jelv.is/blog/Generating-Mazes-with-Inductive-Graphs/
https://github.com/TikhonJelvis/inductive-mazes

Also there's a second haskell based maze generator model on thingiverse:
http://www.thingiverse.com/thing:778556

Old text:
The big and probably very hard one (20x10x3 paths) is inhomogenous!
One side (longest axis) has long pathways with few forks and almost no four five and six-way forks (labyrinthical) the other side has lots of short paths dead ends and more four five and maybe six-way forks (mazeical). There is no sharp border between those regions.
The medium sized one (12x12x2 paths) is
overall more "labyrinthical".

Start with the smaller one, the big one took 7h for me.
Make sure bridging works perfectly beforehand!
Don't hatch fill walls.
Reason in instructions of: http://www.thingiverse.com/thing:15913
Try to avoid fine plastic hair. You wont be able to remove it on the middle layer afterwards. Put a heavy metal ball in, mark the start and finish location to your liking and cap it on both sides with Acrylic or an other transparent material. There are holes for M3 screws to clamp it together. Print it in translucent plastic so that it wont be too hard to use the middle layer.
One could add coordinates on the capping plates like (I/II)-(A..T)(0..9)
And then execute travels like "go from [I-C7] to [II-T0]"