Have you tried Infinifactory (3d FPS ala Portal + assembly lines)? I loved Big Pharma and its not exactly the same, but it felt like the same parts of my brain were working on it.
I liked TIS-100 a lot too, and Infinifactory is kind of like a visuospacial, high-production version of it.
Zachtronics in general seems to be pretty great with this.
I think that distinguishes them from other kinds of puzzle-games where you're hunting for "The One Predefined Secret" to make your solution.