Uncle Grandpa (Uncle Grandpa) possesses the ability to exist as multiple duplicates of himself simultaneous with no clear limit, and can even traverse through other universes.
Eternity (Marvel) is the embodiment of time.
Infinity (Marvel) is the embodiment of space.
The Living Tribunal (Marvel) is the overseer of the Marvel universe.
Schrodinger's (Hellsing) ability of being everywhere and nowhere extends even to very subjective realms.
ZeedMillenniummon (Digimon) is able to fly freely through space and time.
The Master Emerald (Sonic the Hedgehog) is a transcendental object that exists simultaneously in all time lines across the time-space continuum. That means should the Master Emerald disappear in one time frame, it would cause a chain reaction that would make the Master Emerald disappear in all existing time frames.
The Time Eater (Sonic the Hedgehog) is an almighty entity of time.
The Elder God (Legacy of Kain) is "eternally present, here and everywhere, now and always."
After supposedly dying in a Lutece field "accident", Ronald and Rosalind Lutece (Bioshock Infinite) became scattered across the probability space, allowing them to exist through-out time and space within their shared multiverse.
After the machine inhibiting her abilities was destroyed, Elizabeth Comstock (Bioshock Infinite) became omniscient and omnipresent within her multiverse through all of her alternate counterparts.
Spenta Mainyu (Valkyrie Crusade) the watcher of all creation.
Mr Burt/God (The X-Files) displaying his omnipresence by appearing as the entire city.