It's your first day in the shipping plant. You've been given the simple task of sorting out a few colored boxes. How difficult could that be? (For those playing at home, the answer is "immensely.") Great Permutator is a tough-as-a-titanium-statue-of-Steven-Seagal puzzle game by Ripatti Software that will remind you a lot of SpaceChem, in terms of both ingenuity and difficulty.
Dinos in Space is, apart from being a very cool thing to draw in your notebook while ignoring the math lecture going on in your class, a cerebral flow-based logic puzzle game from John Saba. Using arrows, switches and teleporters, your goal is to send dinosaurs from their dispensers into the appropriately colored satellite elsewhere on the grid. Sure, it sounds simple on the surface, but get your head wrapped in this game, and when you take a break, you'll still be solving puzzles in your brain.
In each level of Robot Unlock, your goal is to program a path for your Executor robot to travel around a series of command tiles that alter the robot's stored memory. It's very much like SpaceChem and similar logic/programming puzzle games, only in this little game, you'll be using math more than you'd expect!
Don't be replaced by a robot! Just learn to program robots! Then send them on tasks involving crates, bombs, explosions and junk food in this free logic/programming puzzle game. Pragmatica is a smart game in the vein of SpaceChem and The Codex of Alchemical Engineering.
The creator of The Codex of Alchemical Engineering and Bureau of Steam Engineering (not to mention the grandaddy of Minecraft, Infiniminer) is back with a full-fledged indie game ready to provide a serious logic puzzle challenge. SpaceChem is anything but simple, anything but easy, and one of the most satisfying puzzle games released. If you can solve its challenges, that is. SpaceChem is a game you'll spend a few minutes learning but weeks trying to master, and its 50+ levels are more than enough to strain your poor brain matter more than it's been strained in quite some time.