The Aburame clan of Naruto act as human hives for armies of destruction bugs, who live off their chakra and can swarm and poison enemies.
In Bleach, Ichigo's Hollow powers are the result of the remnants of the proto-arrancar White that had infected his mother Masaki being passed on to him at birth. These remnants merged with Ichigo's natural Shinigami powers which he inherited from his father and became his Zanpakuto Zangetsu.
In Creature Tech, an alien parasite rips Dr. Ong's heart out, then attaches itself to his chest and serves as a replacement heart. It also provides him with several extra limbs, skills in hand-to-hand combat (the thing can learn kung-fu by watching movies), and when Ong gets really upset, teleportation powers.
In Iron Man, War Machine had at one point Eidolon Warwear.
Marvel Comics' Sasquatch, from Alpha Flight, originally thought he was that way due to gamma rays (a laHulk) but it turned out he opened a doorway into another dimension, through which a Great Beast was able to come through and bond with him.
Toxin from Marvel Comics. Venom tries to be this at times, depending on the host (Eddie Brock pulled of a decent Anti-Hero, Mac Gargan faked it, and Flash Thompson is this until the symbiote freaks out and starts eating things). Anti-Venom tries, but Eddie's a little too... off in the head to pull it off for extended periods.
Spider-Man was this during his time with the symbiote.
Severed Ties (1992): a desperate scientist injects himself with a reptile based regeneration serum to return his arm count to two, which worked out fairly well as long as one fed it and didn't mind the teeth, or mouth, or eyes.
Parasite Eve. For the most part, the Neo-Mitochondria (Mitochondria who have developed a Hive Mind sentience) are simply The Virus, but in a few people with just the right DNA (read: Aya Brea) it instead becomes a powerful, symbiotic force, granting Super Strength, Hyperactive Metabolism, Pyrokinesis, and the ability to kill people on the cellular level with your MIND. And probably pick out winning lottery-tickets, too.
Dark Future: Krokodil becomes the Host of the Ancient Adversary, the Pawn of the Nullifiers. Exactly what the nature of the Ancient Adversary is is never made entirely clear during the series. However, it seems to take the form of a crocodile and is connected in some way to the Moon. It's certainly been around as long as Seth and the Dark Ones have and it's probably not good, just antithetically opposed to them. Being it's host gives Jessamyn some degree of supernatural invulnerability and some extra super-strength on top of the cybernetic augmentations she already had.
Seen in Perry Rhodan once in a while. For a time, the eponymous protagonist himself had "Whisper", an intelligent alien symbiont who could be worn like a cloak and in exchange for regular baths in a protein-rich nutrient fluid endowed his wearer with telepathy and enhanced night vision; for another example, part of the entire culture of the Duchy of Krandhor was the common use of "spoodies", tiny insectoid creatures that implanted themselves under the host's skin (usually on top of their skull) and provided a measurable intelligence boost.
A short story titled Idiot's Crusade has an alien quietly fuse with the stupidest kid in town to study humans For Science!. A side effect of this is that the boy gets a massive amount of powers (and total control over them), but without any enhanced intelligence. This leads to a rather disturbing ending, where the boy, in an effort to make the world "happier", decides to go to the UN building to use his powers to improve the moods of the world leaders (while still lacking the mental capacity to think out the effects or ethics of his actions). Meanwhile, the alien realizes there is no way for him to detach from the human, meaning the idiot is guaranteed his powers for quite a while.
Blending with a symbiote in Stargate SG-1 can result in this: the human (or other creature) gains greatly increased healing abilities, a near-perfect immune system, and an elongated lifespan. They also get the sum total of all the knowledge of the symbiote. The downside? They have to share their body and mind with another intelligent creature. The Tok'ra believe that equal sharing of the body between symbiote and host is the proper way to do this, and only take unwilling hosts in extreme circumstances. The Goa'ulddo not share such morals.
Haruto Souma, Kamen Rider Wizard, became a magic-user by resisting his Despair Event Horizon through Heroic Willpower (those who don't are killed and replaced by their own inner Phantoms). Since then, he's made it his mission in life to be the "final hope", preventing others from falling into despair and becoming Phantoms. When his Phantom was destroyed, he ended up bringing it back to life in order to protect his friends, and thus created his Super Mode Infinity Style. For its part, Haruto's Phantom gradually goes from Teeth-Clenched Teamwork (since if he dies, so does it) to actually respecting him and being a willing partner.
Exalted: This is how Infernals are made: a minor demon bearing an Infernal exaltation burrows into the body of the Infernal to-be. The demon (designated as 'Coadjutor') act as bridge between the Infernal and her Yozi patron(s), enabling the Infernal to use Yozi charms. The Coadjutor remains sentient and act as the other voice inside the Infernal's head.
Alex Mercer from Prototype might count, having survived the Blacklight Virus and gotten powers from it. Subverted though, it turns out it's not that he survived but that the virus is him. The guy 'hosting' him was also a complete bastard - so spectacularly evil that the flesh-eating super-virus that ate him was an improvement.
James Heller, same powers, is also an example; perhaps even a purer one.
Shin Megami Tensei: Nocturne has Lucifer inject the main character with a parasitic demon called a magatama near the start of the game, transforming him into a half-demon.
Skullgirls has a couple of these, most prominently Filia, who plays host to Samson (not the one from The Bible). She combines her own fighting prowess with Samson's Combat Tentacles.
Jill Valentine in Resident Evil 5, thanks to the anti-bodies in her system from her T-Virus infection in Resident Evil 3: Nemesis, is completely immune to the mutagenic effects of the countless viruses that Umbrella has spawned. Unfortunately, this is also the reason Wesker's Mind Control chest-thing worked on her without killing her.
Resident Evil 6 gives us Sherry Birkin and Jake Muller. Sherry still carries the G-Virus in her body from her infection in Resident Evil 2: The vaccine she received stopped her from mutating but gave her a ridiculously sped-up Healing Factor. Jake on the other hand has a variant of the Progenitor Virus in his system which he inherited from dear old dad, which boosts his physical capabilities and makes him immune to the C-Virus.
The Seru from Legend of Legaia grant their human host a variety of superhuman powers as part of a mutual fusion, which may include (depending on the Seru) Elemental Powers, Super Strength, or flight. In the presence of the Mist, however, this turns to Demonic Possession; the main character's Ra-Seru are immune to this downside.
In Worm, Every parahuman in existence appears to be an example, as when they get their powers they enter a relationship with a being called a passenger, which gives them access to their powers and makes sure they have the Required Secondary Powers to survive having them.
In MIB: The Series, when a Symbiote attaches to you the upside is nigh immortality via healing/rejuvenation, rubberman-like expansion tied to an epic shapeshifter baggage, varying amounts of shapeshifting for yourself, on and off again ability to breathe fire, and a "lay on hands"-ish ability to heal others. the downsides, however, are that you could get attached to an annoying Symbiote and you have 20 hours before you mergepermanently.