What do damage buffs affect?

overwatch

In Overwatch, there are several ways to buff the damage dealt by a hero: the alternate fire of Mercy's Caduceus Staff, Ana's Nano Boost, and Orisa's Supercharger.
Are they all governed by the same rules? What can they affect, or not affect?

This question exists to have a single reference point for the many, many questions that have been asked, instead of having to update each answer individually when game mechanics change

Solution 1:

All damage buffs work in the same way, affecting the vast majority of weapons and damaging abilities in the game with only a few exceptions.
The power boost is variable, with Mercy boosting damage by 30%, while Ana and Orisa boost damage by 50%.

The only damage sources that cannot be boosted are:

D.Va's Self-Destruct
Hanzo's Dragonstrike
Junkrat's RIP-Tire
Junkrat's Steel Trap
Symmetra's turrets
Torbjorn's turret

Edge cases

For completion's sake, here's a list of interactions that might not be intuitive at first glance:

Projectiles such as Pharah's rockets or Junkrat's grenades will deal boosted damage if the hero is buffed upon impact, not launch.
Genji's Deflected attacks deal damage based solely on Genji's damage buffs, not the original source's. It is not possible to infinitely increase damage by juggling a projectile back and forth between two damage buffed Genji.
The damage buff is reflected in the circles and skulls for McCree's Deadeye. A McCree that is constantly buffed will reach skull icons faster than a non-buffed McCree, but will revert back to normal damage if the damage buff is removed.
All damage buffs stack additively with each other, and they all stack multiplicatively with Zenyatta's Orb of Discord.
Damage buffs do not affect the healing dealt by Ana's Biotic Rifle.

Solution 2:

There are a few rules for damage boosting abilities.

Ana, Mercy, and Orisa's damage buffs stack additively with each other, while Zenyatta's Orb of Discord stacks multiplicatively.
Damage boosts are calculated when damage is dealt. This means heros must be buffed during detonation for abilities such as Pharah's rockets, Junkrat's grenades, or D.Va's Self-Destruct.
Damage buffs have no impact on non-damaging effects such as healing, freezing, or knockback.
Damage boosts of the same type cannot be stacked. This means there is no benefit to 2 Mercys damage boosting a single hero.
Damage over time effects deal boosted damage for as long as the hero is being buffed. This includes Widowmaker's Venom Mine and Hanzo's Dragonstrike

Here is a list of which abilities can and cannot be damage buffed.

Buffed when fired (Hitscan/Melee)

Ana's Biotic Rifle (scoped)
Bastion's Recon and Sentry bullets
D.Va's Fusion Cannons
Genji's Deflect (hitscan)¹ and Dragonblade
Lucio's Sonic Amplifier (secondary)
McCree's Peacekeeper Pistol and Deadeye² (Source)
Mei's Endothermic Blaster (primary)
Reaper's Hellfire Shotguns and Death Blossom
Soldier 76's Pulse Rifle
Sombra's Machine Pistol
Symmetra's Photon Beam (primary)
Torbjörn's Forge Hammer
Tracer's Pulse Pistols
Widowmaker's Sniper and Assault Rifle
Winston's Tesla Cannon and Primal Rage
Zarya's Particle Cannon (primary)
All character's melee attacks

Buffed during detonation/impact (Projectiles)

Ana's Biotic Rifle (unscoped), Biotic Grenade, and Sleep Dart³
Bastion's Tank Mode explosives
D.Va's Self-Destruct⁴ (Source)
Genji's Shuriken and Deflect (projectiles)¹ (Source)
Hanzo's Storm Bow, Sonic Arrow, and Scatter Arrow
Junkrat's Frag Launcher grenades, Concussion Mine, and Steel Trap (Source)
Lucio's Sonic Amplifier (primary)
McCree's Flashbang
Mei's Endothermic Blaster (secondary)
Orisa's Fusion Driver
Pharah's Rockets and Rocket Barrage (note increased self damage)
Reinhardt's Fire Strike and Earthshatter⁵
Roadhog's Scrap Gun (primary/secondary) and Whole Hog
Soldier 76's Helix Rockets
Torbjörn's Rivet Gun
Tracer's Pulse Bomb (Source)
Zarya's Particle Cannon (secondary)
Zenyatta's Orb of Destruction

Buffed over time

Hanzo's Dragonstrike
Widowmaker's Venom Mine (Source)

Cannot be buffed

Ana's healing from Biotic Rifle or Biotic Grenade (Source)
Junkrat's RIP-Tire (Source)
Pharah's Concussive Blast
Soldier 76's Biotic Field
Symmetra's Sentry Turrets (Source)
Torbjörn's Turrets (Source)

Unknown

D.Va's Call Mech
Mei's Blizzard
Zarya's Graviton Surge

Sources

Reddit - Mercy's damage boost works on almost everything as long as the boost is applied when the target RECEIVES the damage
Reddit - Myself and some friends tested some more Mercy damage boost myths!
[PC] Overwatch Patch Notes – July 19, 2016
Overwatch Wikia - Ability (Ranged Abilities)
DanmakuGrazer - What do damage buffs affect?
What ultimates can be damage boosted by Mercy?
Does Mercy's damage buff affect structures?
Is D.Va's ultimate affected by Mercy's damage boost?
How do Zenyatta and Mercy's damage boosts stack?

Notes

¹Applied on-fire for hitscan abilities, on-hit for projectiles. Based on Genji's damage buffs. Buffs cannot be stacked with multiple reflects.
²Killing shots can be made before red circles finish locking on.
³Ana's sleep dart does 5 points of damage.
⁴Beam must be on mechless D.Va to boost explosion damage. See Is D.Va's ultimate affected by Mercy's damage boost?.
⁵Reinhardt's Earthshatter is not technically a projectile ability, but takes a small amount of time to travel