One-way-walls: Interesting puzzle mechanic that also has backroute patching potential.
Water: It looks nicer than a bottomless pit even if it's usually effectively just a reskinned bottomless pit. Swimmers are a thing, too, and I use them sometimes, but they're not the main reason I like this object.
Infinite use traps (both): Lots of potential: you might have to avoid the trap, compress the squad (triggered traps only), or bypass the trigger area by building over it or digging under it. You can also disable them with disarmers, but personally I don't find disarmers very interesting. I don't really care much for the one-time use traps, though.
Pickup Skill: Technically, they do have puzzle potential, but where I like them the most is for addressing backroutes: not having all the skills available from the start can reduce the number of ways a puzzle can be bypassed. Just be careful not to overuse them, though, because that can just give away the solution.
Updraft: It's simple, yet has great potential. It can alter where gliders go, which can be used as a way to move gliders around, or as an obstacle for gliders (maybe the updraft will take them somewhere bad like into the
clam), and the fact that it resets a lemming's fall distance can be used as either a puzzle element, or an anti-frustration feature if the splat height can cause unintended issues (though I'd default to making it smaller before plopping down updrafts most of the time).
Dishonorable mention: Teleporter/Receiver: Unnecessarily confusing when there's more than one pair, even when using clear physics mode.