This is one of those things on the internet that passed me by. Mainly because I was linked to it, couldn't work out how to play it by clicking around it's interface and so didn't bother with it. This has happened a couple of times in the last year, but yesterday when I found myself looking at it yet again (it was mentioned in An Episode Of Geek Nights on Programming) I thought I would give it a proper go. And I am so glad I did.
What I am referring to is a flash game called The Codex Of Alchemical Engineering. In it you are given a set of atom modifiers and some manipulator arms that you must use to collect basic atoms and from level to level make more and more complex elements from them. The game plays very much like a simpler version of CeeBot.
Here is a video tutorial that should help get you started.
NOTE: To rotate one of the arms you have to click and hold the left mouse button as if you where dragging it, and while still holding the left mouse button press the Ctrl or Shift keys on your keyboard to change the arm's orientation or start length. This is not very well explained in the game's instructions, the video does a slightly better job, but still doesn't spell it out.
Some of my solutions:
Level 1 (a very fast solution)