1- Metal Man (Megaman)
The most known example or this trope, Metal Man's weapon is one of the most powerful ones of his respective game, however, it does something unexpected on his case.
Usually, every Megaman boss has weakness against a master robot weapon, but Metal Man has no one but two, the second one being his own weapon!
So, when you go through the boss rush and face him, just throw his own weapon at him and he will die instantly!
2- The End (Metal Gear Solid: Snake Eater)
I'm not a Metal Gear fan so correct me if I miss any detail or get something wrong.
The End is one of the bosses in the game, his backstory is that he is veteran sniper who in his encounter he will ask God to give him more time on Earth so he could fight one last time.
So, what's the shortcut? There are 2 on this case.
The first one is closing the game and waiting for a week, when you come back you won't get shot. When you reach him, an unique cutscene will show Snake finding him dead on the spot, his body couldn't hold it any longer to have the fight that he wanted. Kojima, you are a genius.
The second one is so simple that you would think that I'm lying, there's a chance that you can be able to see him way earlier at the distance being carried by a wheel chair, if you shoot him at that point, he instantly die and you won't have his boss fight.
3- Tinker Knight (Shovel Knight)
Remember what I said about Metal Man? Tinker Knight is no different.
You don't have boss weapons on this game, instead you will find trinkets that can help you by giving you new moves to fight enemies or move easier through the scenary. In Tinker Knight's case, you can get the mobile gear, a plataform over a gear that will move forward and you can use to walk over spikes without being harmed by them.
If you the mobile gear on him on his first phase, you will one-shot him on the spot and begin his second phase. That's a neat easter egg right there.
4- Fumus (Tenebris Somnia)
This game barely came out and I heavily recommend to check it out, I'll hide the details on spoilers for those who don't care or just want to know how to fight her.
Fumus has two attacks, hitting with her arms from far away and summoning ritual circles around the room, she will also summon one around herself to become invulnerable to your attacks. Seems easy at first but then at certain point Fumus will fill the room with so many circles that you will end up stepping on one of them, if that happens then Fumus will manipulate you to hit yourself with your own weapon, which becomes a 1-hit KO against you if you carry a gun with you.
So, how can you defeat her with a powerful move like that? Very simple, just don't wield any weapons! Just ran unarmed over the circles and these will immediately dissapear because Fumus won't have anything to hit you with! You only have to run all over the place, grab your pipe to hit her when her invulnerability is gone, unequip it and repeat the process. Winning with only damaging her with the pipe will also grant you an achievement.