Reis in Final Fantasy Tactics, being basically a Dragon in the shape of a woman, can breathe Fire, Ice, or Electricity. Oh, and Holy. However that works. This may not have been clear in the original translation (Where breath gets translated Braclet)...
All Final Fantasy games where Blue Mages appear feature them learning breath weapons. Usually, three are available: Aqua Breath, Fire Breath and Bad Breath (Malboro's famous chemical weapon grade halitosis attack).
Barthandelus, Big Bad and Master Troll of Final Fantasy XIII, has two ultimate moves named "Thanatosian Smile" and "Thanatosian Laughter," both of which consist of him barfing lasers on you.
Sigma at the end of Mega Man X6, as well as too many other robots to sanely list here.
In V for the Game Boy, Mega Man has spent the game using the Mega Arm, because his Super Mega Buster can't affect this batch of robots. What happened to it, you ask? Dr. Light put it in Rush. He shoots the charged shots from his mouth (having no arms).
Virtually every weapon in Mega Man Star Force that does not simply come into existence in midair is fired from Omega-Xis' mouth. As a result, most of what Mega Man fires is technically a Breath Weapon, most notably the first game's Tail Burner, which is actual fire. Well, digital fire.
Breathing fire is one of Bowser's trademark characteristics in the Super Mario Bros.. series, but there are a few other critters that have this ability (such as the Dino Rhinos and Reznors in Super Mario World).
The Dragon and Dragon Zombie in the Disgaea series predictably have a breath weapon, using fire (Or wind or ice in the first game) and darkness respectively. There's also the Cockatrice, who uses either petrifying breath or miasma depending on the game.
The Pandaren Brewmasters from Warcraft 3 can breathe "fire" (ignited grain alcohol) to a... panda as part of their standard skills, although they are firmly good guys. This also shows up on some of the neutral monsters. There is also a breath of frost, but it shows up much more rarely.
Dragons in the same games also have breath attacks. Red dragons breathe fire, black ones breath molten lava, blue ones breath ice or magic energy, green ones acid and in World of Warcraft bronze ones breathe magic, superheated sand that causes rapid aging, although in Warcraft 3 it's clearly lightning.
In World of Warcraft, almost all Dragon-type bosses, in addition to regular bolts and fire/frost/poison/whatever else breath have a devastating attack that begins with: "X takes a deep breath..." and generally must be avoided via some sort of trick. Black dragon Onyxia is mostly infamous for her insanely powerful Deep Breath which she uses completely randomly, which makes it hard to avoid. For months, if not years, people have tried to come up with explanations of what makes Onyxia Deep Breath more. Some theories make more sense than others, but all are false. It's really random.
Ironically Onyxia is also a subversion of this trope, since her Deep Breath flames seem to come straight from the ground instead of her mouth, perhaps due to graphic limitations?
Chimeras have one head that spits acidic bile and another that breath's magical lightning.
Hunter-pet Chimeras in World of Warcraft breathe frost and lightning. Even if the non-tamed mob has a poison/acid ability as a mob (which it loses when tamed).
Frost Wyrms have an ice breath weapon.
Though, since Frost Wyrms are giant reanimated dragon skeletons, its debatable if this can be called a "breath" weapon (what with them not having actual lungs and all).
Beginning in his first game, Kirby could spit puffs of air with enough force to damage most enemies, and power-ups allowed him to spit puffs of minty-fresh or spicy-hot breath. In later games, after he learned to steal enemy powers, he could gain the ability to exhale fire or ice.
Spyro the Dragon isn't limited to merely fire breath - he goes as far as to launch ice, earth chunks and electricity out of his mouth. Cynder uses shadow, wind, poison and fear.
He can only launch chunks of earth if he scoops them up in his mouth beforehand. It's not a breath weapon, it's just spitting.
The daedroth and spider daedra in The Elder Scrolls IV: Oblivion. The daedroth spits balls of fire; the spider daedra breathes lightning, and also casts a touch-range paralysis spell by exhaling green haze into its palm and then slapping the target.
Jak III's Dark Makers have access to giant stompy Humongous MechaSpider Tanks. How could you make this kind of combo even worse for Jak? The head can fire a laser from where a mouth would be on an organic creature.
In Lost Souls MUD, a number of species breathe fire by way of phlogiston glands. Esoteric breath weapons are explained by phlogiston absorbing magical essences that infuse the glands' owner.
Breath attacks form a skill family in Dragon Quest. The weaker versions are pretty common among low- to mid-level monsters, while the most powerful breath attacks tend to be spammed by bosses. (Especially the Final Boss.) Later games allow the player to recruit monsters or use special character classes that have access to these abilities. What makes them particularly obnoxious is that despite dealing elemental damage, they don't count as magic attacks, so the only ways to protect yourself from them are with equipment, spells or skills which either reduce damage taken from those elements regardless of the nature of the attack, or specifically defend against breath attacks.
Monster Hunter used basically every Wyvern, Dragon, or "Boss" monster plus a few minor enemies. Yian Kut-Ku, Rathalos/Rathian, Yian Garuga, and if you want to be technical, a King Shakalaka all have a fire-based breath attack. Mostly fireballs, and in the case of the Yian Kut-Ku, it is simply lobbed out. The Gravios and (more rarely) Basarios have a beam-like weapon that also has an Exhaust after-effect, where they are likely to burn everything within melee range of them after disintegrating you with their throat laser. Among the -prey series there is Giaprey and Ioprey which spit ice and poison based attack respectively. Hypnoctrice has Sleep- based attacks. Congalala, Teostra, and Leostra all have flamethrower-esque attacks.
Tri ups the ante considerably. Rathalos and Rathian still spit fireballs, but Rathian can spit three at once or a "blaster" which blows up everything a good ways in front of it. There's also the Qurupeco, which spits an oil-like substance as one of its attacks; the Royal Ludroth, which spits water; the Gigginox with poison; the Baggi and Great Baggi with sleeping agents. Up until now, it was sensible. But then there's the Lagiacrus, which shoots ball lightning from its gaping maw, the Barioth ejects a miniature blizzard as its breath weapon, and the Agnaktor fires what is essentially a heat beam!
Which doesn't actually mean it ups the ante, as many monsters in previous games could also do things like that. Khezu could spit electricity, and Gravios's sweeping heat beam was absolutely infamous.
Ceadeus launches a powerful stream of water and Alatreon launches ice breath
Battle for Wesnoth's Drakes are all capable of breathing fire although one caste (the Clasher unit line) gives up this ability in favour of the protection provided by heavy armour, which restricts their breathing enough to prevent this.
Among the power-ups in Gauntlet Legends and its remake Gauntlet: Dark Legacy are breath weapons, including Fire Breath, Acid Breath, and Lightning Breath. Unlike most of the power-ups, these have ammo-based usage instead of being active for a limited time. A lot of the bosses use breath attacks too. Even though there's no Light Breath power-up but there's a Light Amulet, Skorne can spit beams of light at you.
Pokémon features a few moves like this, namely Dragon Breath and Frost Breath. The anime expands on this making many attacks mouth-based.
The final boss of Mass Effect 2 is a gigantic partially-complete Human Reaper that attacks with a gigantic, long-charging beam attack from its mouth. It's also its own worst enemy with the thing, often sweeping its allies off the platform for you.
Nethack has dragons of nine different colours, covering each of eight different breath attacks (silver and white dragons both use cold breath). Hell hounds, winter wolves, iron golems and Nazgul can also breathe (fire, cold, poison and sleep respectively); and then there's the Chromatic Dragon.
Alisia Dragoon uses it for several things, including Dragon Frye's fire, the fireballs spat by the Stage 4 boss, not to mention the various things such as sparks and worms that come out of Baldour's mouth.
The dragon in Dra Koi fires mouth beams as both a dragon and in human form, at which point her eyes glow and she grows huge fangs.
In Pikmin the enemies Fiery Blowhogs and Watery Blowhogs breath fire and water respectively.
Higher-level skags in Borderlands have fire and laser breath, as well as spitting shock and acid.
Awakening: The Sunhook Spire introduces special dragon altars for Sophia's pet pocket dragon that can allow it to exchange its normal fire-breathing for other elemental powers through its breath.
Ryoufu from World Heroes can take a chug of alcohol and then spit fire on his opponents.