In Baki the Grappler both Dorian and Che Guevera know a trick where they take hair from their beard and blow it into an opponent's eye with dart-like accuracy. It does no damage but stuns any opponent it hits due to the sensitivity of the eye.
Ishida's fight with Cirucci Sanderwicci finishes when he fires an arrow made of a chainsawlightsaber.
Riruka's gun fires miniaturized objects that enlarge in midair.
A gun wielding quincy fires bullets of reishi that look like the quincy cross and can set fire to people.
Blood+: Kai has a gun that fires delayed exploding bullets, with the last bullet of each magazine triggering the others to explode simultaneously. This is used to overcome the Chiropterans' substantial Healing Factor. It can still only slow them down.
In Digimon, the Garbagemon wield bazookas that fire faeces at their targets.
Et Cetera is about a girl with a gun that shoots the essence of the animals in the Chinese Zodiac. The gun is powered by rubbing the barrel against any item that is made from the animal represented in the zodiac — including a bikini made from Tiger skin.
Eyeshield 21: During the "Tower of Hell" chapter, Hiruma uses bullets that are actually pellets full of desiccant powder, designed to make the ice being carried by the candidates for a spot on the Devil Bats melt faster.
In Fist of the North Star, there is a technique in the Nanto martial arts that involves launching the practitioner out of a cannon while they hold a sword.
FLCL: Canti's gun uses Naota himself as ammo, albeit rolled into a flying, glowing red ball.
An assassin used a unique weapon against her wealthy target: a shotgun, built into her forearm, that fires rolls of coins.
In the episode "Testation", a rampant Spider Tank — which had dodged or neutralized everything else thrown at it — gets stopped by a gun that fires canisters of some kind of quick-hardening glue. Gumming up the tank's legs being the only means of stopping it, short of using weaponry too powerful for use in an urban area.
Togusa used a tracer bullet loaded into his Mateba Autorevolver to tag a fleeing car.
Heat Guy J: Perhaps as compensation for only ever being issued six bullets, Daisuke is usually provided with one devastatingly explosive "Red Cap" round.
Alucard's first gun fires 13mm explosive steel/silver alloy rounds (the silver is also melted from the cross of a cathedral), Victoria's Harkonnen fires 30mm armor-piercing depleted uranium/silver alloy or incendiary shells, and the Jackal fires explosive shells encased in Macedonian silver with mercury tips.
Alucard: It's perfection, Walter.
In the last episode of the anime he manages to pull off firing actual melted silver from a cross with his half wrecked gun. He manages it because he is Alucard.
Hunter × Hunter: Ikalgo uses an airsoft sniper rifle to fire huge fleas (which somehow survived the brutal impact) to make the victims bleed to death due to their bites preventing coagulation.
Mista from Part 5 has a colony Stand called Sex Pistols. He uses ordinary bullets, but his Stands (named "1", "2", "3", "5", "6" and "7") can fly and deviate the trajectories of bullets (with kicks), making it possible to Mista to hit targets beyond a corner, to say one. At least one time some of them ride a bullet to reach the target faster, although they never strike him on their own.
Part 4 has Yoshikage Kira combining the power of his Killer Queen stand and that of Stray Cat's to create invisible shots of air that explode.
Part 7 has Johnny Joestar shoot his own fingernails via his Stand, Tusk.
Kill la Kill: Taken to its extreme. Name it, and it's almost certain that it will be weaponized at some point.
Tsumugu's weapons of choice are sewing machine guns. They fire acupuncture needles that can disrupt Life Fibers, or cure the ills of people.
Being a Merchant City, the Osakan students use money as their ammunition.
There's also the Disciplinary Committee's iron clad rulebook, capable of destroying a tank when thrown at it.
Kurohime takes this trope outside to shoot it in the head.... with a DRAGON
Macross 7's Nekki Basara pilots a robot that shoots speaker pods (thoughtfully loaded with glue so the target won't be killed by cockpit depressurization) and sings to his aggressors, hoping to make them give up fighting. He also keeps in reserve a scaled up cannon larger than his own machine for use on battleships.
Magical Girl Lyrical Nanoha StrikerS: Teana has Cross Mirage, a pair of handguns that shoot magic. From the same franchise, there are Cartridges, which are condensed magic in what looks like a firearm shell, but these are not actually shot, just exploded to supercharge a Device.
Magic Kaito: Kaitou KID has a gun that shoots cards.
Haruhi Suzumiya: In The Melancholy of Haruhi Suzumiya, Haruhi subconsciously modified model guns into firing pressurized water balls with unimaginably explosive firepower. Dual squirt guns turned dual mini water-grenade launchers/pistols.
Mobile Fighter G Gundam: Late in the show, Chibodee and George are facing off against one of the Devil Gundam's Four Kings when they start running low on their respective ammo (Gundam Maxter's revolver bullets and Gundam Rose's Attack Drones). They decide to pull off a Death or Glory Attack, George running interference while Chibodee uses the last Attack Drone as a bullet and aims for their opponent's cockpit.
Negima! Magister Negi Magi has Magitek bullets able to alter space-time at the point of impact. They were used to send people three hours into the future, but it's implied they can also displace the target to a nearby location. Negi used magic blast guns and strip laser beams.
Mr. 5 loads his revolver with his BREATH. However, his devil fruit power let him make any part of his body explode, breath included. How he was able to tell where his breath bullet was after fired, we'll never know.
Usopp uses pachinko balls for his slingshot Kabuto and whatever he could get his hands on prior to that (Rotten eggs, Tabasco balls, small rocks...). After the Time Skip, he uses Pop Greens, insta-growing plant seeds. But that pales in comparison to the most unusual ammo he ever used. A drawing of his earlier Nightmare Face that caused his enemy Sugar to pass out. So he, (with help from an artist) made a projectile that would fire a replica.
Katakuri is particularly fond of jelly beans, so he shoots people with them. He doesn't even need a gun—he just flicks them, and they'll rocket right through people's heads.
Outlaw Star had 'Caster Shells' — magic in a bullet. Special mention goes to Number 4 shells, which fire miniature black holes. Their effect on Gene's unfortunate enemies produces some of the more frightening scenes of the series. What they do to Gene when firing them isn't exactly pretty either.
Reborn is an adorable baby mafioso who has a gun that, if shot in the head by it, you die. And then come back to life, in your underwear, for five minutes, with the ability to complete your life's ambition. If you complete said ambition, you get to continue living. If not, you perish. Again.
Xanxus and Gokudera also have guns that fire Dying Will Flames (although Gokudera's is more of an Arm Cannon). Xanxus uses his own Flames of Wrath as ammo, while Gokudera loads his gun with dynamite.
Rebuild World: Akira eventually gets a sword that works by pouring out liquid metal into a force-field to customize its shape to fit the situation, to make up for his previous sword ending up a Wrecked Weapon; with this sword, each blade is meant to be disposable. Akira's Virtual Sidekick Alpha reprogrammed it at one point to form a barrier around Akira and his Cool Bike to survive a Macross Missile Massacre.
Rosario + Vampire: Tsurara Shirayuki uses ice bullets to snipe people. They melt, leaving no evidence.
Sonic X: The Sonic Power Cannon fires the title character as its ammo. Shadow is also fired from it twice (once by himself as an attempt by Tails to save Cosmo from being killed by him, and the second time is when Shadow willingly goes into the canon with Sonic and he accepts the help, knowing that they both may not survive the attack on Dark Oak).
Soul Eater has Death the Kid and his twin guns, the Thompson Sisters, who can fire condensed bursts of Kid's own soul at enemies.
Tegami Bachi: Letter Bee has the titular Letter Bees (postmen with special training to fight enormous monsters) tote around a special kind of gun that shoots a fragment of their "Heart", something equivalent to their life force in this series. They're important because Letter Bees drag letters around a dark, miserable world where 70% of the land is crawling with giant almost-invincible monsters in order to do their jobs...
The main character Yusuke Urameshi and his Rei/Spirit Gun.
The character Sniper has the ability to embed his spirit energy into any object and fire it with the velocity of a bullet, generally making said objects much stronger in the process. Ammunition used includes: pencil erasers, dice, marbles, blades of grass, rocks, an absurd amount of knives, and A GODDAMN TRUCK. However, when he's done screwing around he justopts for a gun. The gun had a particular function: the truck was loaded with fuel (why Yusuke had not destroyed it yet), and the bullet blew it up in Yusuke's face.
