Telekinetics may be able to disable the homing projectiles from coming to them.
Users of Force-Field Generation or Intangibility can defend themselves and avoid the homing projectiles, though they must keep such defenses active at all times as long as the projectiles are still active.
Destruction of projectiles will stop them from hitting, including causing two of such projectiles to hit each other.
Must at least take the initial aim at the target (cannot just fire in some random direction and expect the projectile to automatically home in on the target, unlike targeting), meaning the user's first aim is still as crucial as any normal shot.
Krana Ja-Kal (Bionicle)
Odd Della Robbia (Code Lyoko); temporarily
Yumi Ishiyama (Code Lyoko): temporarily
Saint of Killers (Preacher)
Darkseid (DC Universe); via his Omega Beams
Robin Hood (Robin Hood: Men In Tights); via Patriot Arrow
Durham Glaster (Black Cat)
Hana Mutou (Captain Earth)
The Shot (Cardcaptor Sakura)
Cross Marian (D.Gray-Man)
Navimon (Digimon Universe: Appli Monsters)
Various Characters (Dragon Ball series)
Welfin (Hunter x Hunter)
Aisho Dainenjiyama (JoJo's Bizarre Adventure Part 8: JoJolion); via Doobie Wah!
Kamen Rider Double LunaTrigger Form (Kamen Rider W)
Vander Decken IX (One Piece)
Monkey D. Luffy (One Piece)
Lyserg Diethel (Shaman King)
Kaname Hagiri/Sniper (Yu Yu Hakusho)
Zoboron (Zatch Bell)
Gruntilda Winkybunion (Banjo-Kazooie)
Grand Mages/Wizards (New Blood Interactive's DUSK)
Alexander (Final Fantasy IX)
Alien Controllers (Hλlf-Life series)
Pit (Kid Icarus)
Robin (Iconoclasts); via Stun Gun
Aqua (Kingdom Hearts series)
Riku (Kingdom Hearts series)
Roxas (Kingdom Hearts series)
Sora (Kingdom Hearts series)
Terra (Kingdom Hearts series)
Vanitas (Kingdom Hearts series)
Ventus (Kingdom Hearts series)
Young Xehanort (Kingdom Hearts series)
Sektor (Mortal Kombat)
Any Pokemon using Lock-On or Mind Reader (Pokemon)
Cross Marian's (D.Gray-Man) Judgment fires destructive bullets that do not stop until they hit the target that he aimed them at.
Super Buu (Dragon Ball Z) uses the Human Extinction Attack after he saw how many humans were left, every blast homing onto what he counted.
Android 13's (Dragon Ball Z) S.S. Deadly Bomber homes in on its target.
The Nihilanth (Hλlf-Life) can create portal orbs that lock onto the targets, though they don’t exactly harm them.
Alien Controllers (Hλlf-Life series) can project energy balls that can chase down opponents from their heads.
Pit's (Kid Icarus) arrows have homing effects, the level of it depends on the bow he used to fire from.
Sektor (Mortal Kombat) firing homing missiles.
All Decken (One Piece) has to do is touch his opponent and anything he throws…
…will home in as a deadly projectile…
…to even the gigantic ship Noah.
Saint of Killers (Preacher)
Vores/Shalraths (Quake series) can create and throw energy pods which follow their victims/enemies until they detonate upon impact.
Wraths (Quake: Dissolution of Eternity) can throw projectile balls that float towards their targets and explode on impact.
Inklings (Splatoon) can use Seekers...
...which hone in on any enemy they aim at.
Agent 3 (Splatoon)
DJ Octavio's (Splatoon) Octobot King fires rocket fists...
...and octomissiles that automatically hone in on Agent 3. However, if Agent 3 damages them enough, they'll reverse and hone in on Octavio.
Unlike the regular Mages that project fire balls that can only just be thrown at enemies/victims, the Grand Mages/Wizards (New Blood Interactive's DUSK) can throw large fire balls that home in on their foes.
While in his Gear Fourth - Boundman, Monkey D. Luffy (One Piece) can use his Gum Gum/Gomu Gomu no Python, a semi-homing attack.
Freischutz (Valkyrie Crusade) manipulates magic bullets and make them always hit her targets.
Kaname Hagiri (Yu Yu Hakusho) marks Yusuke and all projectiles he launches will strike the bulls-eyes without fail.
Darkseid's Omega Beams (DC Universe) are capable of tracking their targets across space and time and will always eventually hit what Darkseid wants them to hit. Only one character in the entire DC universe has ever dodged them.