What games do this?
In Ratchet and Clank Going Commando during the Clank stages there's a specific microbot you can use called a Lifterbot that lifts things out of the way for you. He only appears on this single planet he's introduced on and never again in the entire game.
The super useless levitation ability some metroidvanias had.
Even a fangame has it.
Metal Gear Solid the Phantom Handjob.
It was apparently going to be usable throughout the game in the same way D-Walker was but was apparently seen as majorly unbalanced so was cut.
It made me sad that all you could use it for was one level and to farm 1-ups in the observatory.
I'd estimate that they intended to use the feature more often during development, but circumstances led them to drop it.
Going Commando actually has a developer commentary up on Youtube, they might explain why that guy only appeared once but I'm not certain.
As far as I know it was due to playtesters not liking it. Which caused it to be dropped in later levels.
Final Fantasy Tactics
He shows up as an AI guest in one story mission and never shows up in missions again. It isn't even an important story mission. You're just fighting some random thieves at their hideout in the middle of nowhere.
The spinny spike thing in Twilight Princess.
There's not really very many Clank sections in the games in general. I always remember Going Commando's sections to be more tolerable than than in the other two games. Orxon is definitely awful, way too long and boring and I remember the ice section in UYA being pretty shitty too.
There's probably some gadgets or items in the series that were rarely used too, though honestly a lot of them were never all that fun anyway. The hologuise is the fucking worst.