I applied the tags based of the following vague definitions with the knowledge that these categories often cross over:
Programming: The game uses either written code or a visual language to enable to you define behaviors.
Automation: The game encourages you to build up systems which then can work autonomously and then become building blocks for further progress.
Optimization: The game gives you multiple objectives which require you to engineer solutions differently such as for speed or efficiency.
Logistics: The game focuses on movement of elements around the game area and acting on those elements (joining, separating, modifying) those elements in synchronization to achieve a goal.
The recommendations are based solely on what I enjoyed the most. It doesn’t mean the others aren’t good, I may just not have played them yet. A lot of these I haven’t played. The ordering is pretty arbitrary I’m afraid and isn’t necessarily any indication of how good a game it. I may have an unhealthy attachment to Zachtronics games though! 🙂
Full disclosure: I backed both Autonauts and LogicBots on KickStarter.
Lastly, this list is primarily intended for puzzle games and whilst a lot of other games have the ability to build logic or use wiring to solve problems, they won’t be included on the list just because they are primarily platform or survival games, so no Little Big Planet, Minecraft or Terraria I’m afraid.