Clayface (DC Animated Universe) remerging with his fission spawn Annie.
Pinhead (Hellraiser) being remerged with his original human self, Elliot Spencer.
Sora (Kingdom Hearts series) becoming whole by remerging with his Nobody Roxas...
...and Kairi with her Nobody Naminé.
After being infected by a Web Creature, Megabyte (ReBoot) remerged with his sister Hexadecimal...
...to reform their original self, the Super Virus Gigabyte.
Ebony (Sonic the Comic) has recombined Sonic and Super Sonic into one being.
Tiger Talisman (Jackie Chan Adventures)
Rei Ayanami (Neon Genesis Evangelion) after merging with Lilith and removing the AT Fields that maintain individual physical form. Causes the entirety of mankind/Lilin (an already fragmented and self-divided angel) to merge into one being.