Don't get Supergirl angry. You wouldn't like her when she's angry
Rare example of a human with a Breath Weapon, but no "taint": Fire Lad, of the Legion of Substitute Heroes, has the ability to breathe (and sneeze) fire. (Too bad he also has a raging set of allergies.)
Jack Kirby's Demon, Etrigan, breathes Hellfire from his mouth. It tends to function as normal, extremely hot fire, flames that burn one's soul, and infernal fires that destroy pure evil beings. It is of course, magical in nature.
Superman has arctic breath (essentially gusts of supercooled air which tend to freeze things in their path) and heat vision; as a counter to these, Bizarro has "freeze vision" and "heat breath", which is a nice way of saying that he breathes fire.
Superman also has heat breath, although he seldom uses it. In Krypton No More Superman blasts a super-villain with a blow of super-heated air when they fight in the Fortress.
Superman (and, of course, all other Kryptonians and Daxamites) also possess hurricane breath; that is, they can create and direct gale-force winds simply by exhaling, without the winds necessarily being freezing cold. Pre-Crisis, Superman and Supergirl had such precise control over this power that it basically became telekinesis.
Supergirl: The same as her cousin, Supergirl has freezing breath, hurricane breath and heat vision.
In her first self-named series, Kara uses her freezing breath to put out a burning meteorite (Supergirl #4). And in Supergirl #7, she soaks two super-strong cavemen and then petrifies them in ice with a blast of super-cold breath.
In Supergirl Volume 2 #23, Linda uses her hurricane breath to push bystanders away the battlefield.
In Supergirl (Rebirth), Kara uses her super-icy breath to freeze the fist of a train hijacker who tried to punch her.
IDW's Transformers comics have featured Megatron, seemingly spontaneously, developing or formatting new abilities just because of the raw power at his disposal with Ore-13 ("ultra-energon"). Among these is a Breath Weapon. He loses these powers after he runs out of fuel and never uses the stuff again (as he found out that it came with some dangerous side-effects). Cybertronians with bestial alt-modes, like the Dinobots, Monsterbots, Horrorcons, and Trypticon also have breath weapons, and the Dinobots and Trypitcon are explicitly noted as being tainted compared to standard Cybertronians (in fact, it was contact with Trypticon's body-fluids that tainted the Dinobots).
Lesser known Batman villain Fright can exhale fear toxin.
Iron Man's rogue Fin Fang Foom is a fire breather of sorts. He blows out gas that can be ignited.
One of Richie Rich's enemies, the Onion, uses onion breath as his weapon, even making it powerful enough to destroy walls.
In similar vein, supervillian Superciuk note which means something like "Superdrunk" or maybe "Superalkie" from the Italian Alan Ford comics uses his high-proof breath to put his opponents into an alcoholic coma.
Doctor Doom in Ultimate Fantastic Four has the ability to exhale toxic/corrosive fumes as part of his transformation. Apparently, it's based on the fact that his now-useless organs were rotting into mush inside his body.
Played with in Gold Digger. Sliding up the scale, Iron and Copper dragons have fairly generic elemental breath weapons, usually fire. Golden dragons are renowned for having completely random breath weapons, which are affected by their magical auras as well. At the top of the peak, Platinum dragons don't have breath weapons at all, but rather "ether vents", which are essentially small points on their body that can channel destructive levels of magic effortlessly (when used for attack, Word of God has compared them to Star Trek ship phasers.)