Okay here we go for this list broken down by each Doctor and mind you not all everything, but just some of the stuff.
Doctor Number One
Tries to kill a guy with a rock whilst he is sleeping, convinces a crowd to stone a guy, smashes a guy's head in with a shovel.
Also happily leads the Thals into a war with the Daleks, batters a roboman with his stick, and uses a bomb to blow up an entire city with Daleks and Mechanoids. Plus operating a time destructor to destroy an entire planet of Daleks.
Doctor Number Two
He gives thousands of Daleks a power overload blowing them up, sucks an entire Cyber fleet into space, and then the sun. Also, he melts an Ice Warrior spaceship and kills them all. Also uses some makeshift heat lamp gun to kill an Ice Warrior, possibly more than one.
Electrocutes a Cyberman after tricking him to come forward.
Blows up a Cyber invasion army, guns down a Cyberman with Vaughns weapon.
Tricks an Ice Warrior fleet into flying into the sun.
Doctor Number Three
First, this Doctor would frequently engage in fist cuffs against his enemies and win.
He thanks the Brig for shooting a Silurian in the back, kills three Primords with a fire extinguisher, or tries to murder the Master, even when he agrees to flee, by trapping him in a place that's about to get hit by a bomb.
The Doctor actually gets angry at the Brig for not shooting a bad guy earlier "Thank you Brigadier, but for once could you arrive before the nick of time!"
Guns down an Ogron and thanks the Brig for shooting another Ogron, with tricking the Daleks into coming into a house where they are blown up.
The Doctor shoots Ogrons that try and break into the prison ship. Also kills a Dalek by throwing rocks on his head, kills more two Daleks by dumping them in molten ice, and wipes out an entire Dalek base with Ice volcano.
In another episode, he gives the city of the Exxilons a nervous breakdown which causes it to crumble, and in another episode burns several Ice Warriors to death using the "spirit of Aggedor."
Again, that's just some of what The Doctor did for his dark actions.
The Fourth Doctor
Let's see blows up a Zygon base and is happy for the Brig to shoot their leader Broton dead, in different episodes poisons Professor Solon to death or beats a guy up so badly he ends up in the hospital.
Also, in a different episode, The Doctor sends the Master down a bottomless pit and says he hopes he is dead.
In The Talons of Weng-Chiang is The Doctor quite happily gets a gun to shoot a giant rat and later grabs Magnus Creel and throws Creel into a machine that drains his bodily fluids and turns him into a burnt-out husk. Even mention about causally fighting in a war against Creel in the fifty-first century.
The Doctor is happy for Leela to blow up and knife her enemies or using a poison dart when saving his life. Even explains to Leela where weak points for knifing a Sontaran to death.
In different episodes, Tom Baker's Doctor shoots a fendahl, along with vaporizing a Sontaran to death with his gun and kills the leader of the Sontarans invading Gallifrey with his gun.
Also, in other episodes wipes out an entire Movellan invasion force, makes Davros blow up an entire squadron and smiles about it by driving a gigantic rocket into the heart of a Vampire, killing it and its three servants.
Plus, this Doctor like number three and later six had no problem getting into fistfights to protect himself in certain episodes.
The fifth Doctor
Yeah, Mr. celery stick and ironically the Tenth Doctor's favorite regeneration as revealed in the Time Crash mini-episode used his guns when needed without issue.
Like first used a handgun alongside a UNIT solider to put a lot of bullets into some aliens, shooting a Cyber leader, shooting Omega or pushing a Dalek out of a window, and shoots him later.
In other episodes wipes out invading Silurians, blows up several Daleks, and kills more with the Movellan Virus. And the fifth Doctor burns the Master to death (obviously doesn't stick.)
Doctor number six
Yeah, he kills various members of the Cyber squad with a gun, sends two bad guys into acid, and shoots another. In a different episode shoots the Borat, shooting Dalek eyestalk, and gets Peri to blow him up.
Also poisons Shockeye killing him, with tricking a Sontaran and Jacqueline Pearce into using a machine that blows them up.
Doctor number seven
Let's see blows a Dalek up with Ace's Nitro Nine by himself, is happy for Ace to blow up Dalek with a rocket launcher. The Doctor tricks Davros into blowing up Skaro plus talking a Dalek into killing itself
Other episodes have him blowing up the entire Cyber fleet, burns two Cybermen to death, plus gets Ace to destroy their ship using Nitro Nine, and is happy for her to kill scores of the Cybermen with a slingshot.
Also, The Doctor convincing the Haemovore to kill Fenric with his own gas, or tricks Light into killing himself.
Plus was going to shoot the Destroyer before the Brig knocks him out and does it himself.
Like I said The Doctor is a dark person who despite wanting peace won't hesitate to use violence with picking up a gun or whatever other objects he can get his hands on to protect himself or others, then discards said tool.
Again, he mostly uses his wits but there are times he did use a gun in the classic series without a big deal being made over it.
For example, of new series BS produced by Russell T Davis, you guys know the episode in series 4 for Unicorn and the Wasp? Originally, the Doctor rammed the Vespiform into the lake with the car that he and Donna had commandeered.
David Tennant objected because he was concerned that that ending would portray the Doctor as a murderer.
Are you kidding me? RTD, or David you can pretend The Doctor is some pacifist, who judges anybody who does kill or use guns while being a massive hypocrite for all your bullcrap but you don't know who The Doctor is.
Because 50 plus years of the show proves otherwise, I mean heck even Steven Moffat went back to this and had the twelfth Doctor using Venusian aikido (which is fictional and what the Third Doctor first used) again. Which is something Chris Chibnall continued in one episode that I know of.
RTD and David Tennant did you guys sit down with George Lucas for his Han can't kill Greedo in self-defense since that's too far, but Vader a child killer can get redemption on piecing together whatever mess you've made.
Until next time