TIS-100 and Infinifactory (both by Zachtronics) are two of my favorite puzzle games.

Infinifactory looks a lot like Minecraft and has you build factories to automatically build things (as a side note, it isn't copying Minecraft's look, it's the other way around. The same creator's previous game Infiniminer inspired the look of Minecraft).

TIS-100 has you programming a fictional '80s computer in assembly. It's weird as hell, and is one of my favorite games ever.