Hello there. First of all, awesome game! A couple of suggestions:

• I assume the ordering of the levels is intended to be easy on the left to hard on the right. Seems like a couple of them are out of place, eg the generals level is trivial but it's way over on the right (and has a really big work area)!
• Simple examples of accepted/rejected input or transformations (depending on the level type) would be really useful. Not sure that there's room in the UI, so maybe they could go in the ? menu (which admittedly is also full atm )
• The level names have no real meaning (or at least not to me :D), so it's difficult to find one you remember doing earlier (I can only remember the content of the levels, not the names)
• The way you delete things wasn't obvious, maybe you should add that to the help screen, or add a garbage can icon to the UI (which would have the same effect as clicking on the background)?
• The ability to "single-step" the machine might be useful (although I guess you can sort-of do that with the pause button)

Also, the robotic polar bears level won't accept my machine . It says "This robot should have been accepted, with an output string of (Blue, Yellow, Blue)! Input was (Blue, Blue). Click to continue!" My machine (go-go gadget size=1pt http://pleasingfungus.com/?lvl=26&code=y12:2f3;y12:3f3;q13:4f3;q12:4f3;p12:5f3;r13:5f3;b11:5f3;y12:6f3;c11:6f2;c13:6f0;p12:7f3;q13:7f7;b10:9f2;b12:9f2;r14:8f0;r12:8f0;y12:10f2;c13:10f2;c14:10f2;c15:10f2;y14:7f1;r14:6f2;p15:6f1;b16:6f0;c16:10f1;c16:9f1;c16:8f1;c16:7f1;c11:7f3;c11:8f3;c11:4f0;c10:4f0;c9:4f3;c9:5f3;c9:6f3;c9:7f3;c9:8f3;c9:9f3;c9:10f3;c9:11f3;p10:12f2;y9:12f2;r10:11f3;b10:13f1;q12:12f2;c11:12f2;p11:9f3;p13:8f5;q11:10f1;q15:5f0;p14:4f4;y15:4f0;b14:5f1;r14:3f3;) does output BYB for the first robot!
Anyway, keep up the awesome This could be a really good educational game (why does that always sound so cheesy?) for comp sci students...