Universes you can go to more than once by virtue of having more than one Jump send you there.
- Avatar (Avatar The last Airbender, Avatar legend of korra)
- Bomberman 64 (original, Bomberman 64 Second Attack)
- Dark Cloud (original, Dark Cloud 2)
- Deus Ex (original, Deus Ex: Human Revolution)
- Devil survivor, (original, DS2)
- Dragon Age (Origins, Inquisition)
- Exalted (Dragonblooded, Mortal gauntlet)
- Fire Emblem (Fire Emblem Awakening, Fire Emblem Fates)
- Halo (Original, Project Freelancer, the Halo gauntlet, Halo covenant)
- Mega Man (MMX, MM zero, MM battle network, MM classic)
- Metal Gear (Metal Gear Solid, metal gear rising)
- Star Trek (original, TNG+DS9)
- Star Wars (KOTOR, Clone wars, Original Trilogy & 'to be released' SWTOR)
- Starcraft (Terran, Zerg & 'to be released' Protoss)
- The Legend of Spyro (LOS, Legend of Spyro: skylanders)
- Warhammer 40,000 (Light of Terra, Imperium, Eldar, Commoragh, Freelancer)
- World of Darkness (VTM:Bloodlines, V:TR, Mage The Awakening, Changeling The Lost, NWOD Mortals)
- XCOM (original, XCOM 2)
Alternate Universes?
- Bioshock? (original + infinite)
- DC? (DC, Young justice, Green lantern the animated series, Batman Dark Knight Trilogy?)
- Fate? (Fate-, Fate-Extra)
- Fire Emblem (original, awakening & fates)
- Gundam? (?)
- Lego - Lego/Chima/Bionicles, visiting Lego versions of DC, Marvel, Jurassic Park, Star Wars?
- Marvel? (Marvel Comics, Marvel Cinematic Universe, Earth's Mightiest Heroes)
- Super Mario (original, RPG)
- The Elder Scrolls (TES, Skyrim, The Great Game gauntlet)
- Final Fantasy XIII? (original, FFXIII-2, FXIII-3)
"Free Pick" Settings
The Slice of Life jump, Generic Parenting, Horror Movies and the King Arthur jump have the potential to be set in settings you have visited before. For example the King Arthur jump can be set in any version of the Arthurian legend (theoretically visiting the Fates universe, or the Merlin BBC universe, or possibly even DC).
The Horror Movie generic jump can be used to access The Dead Rising universe (as Dead Rising: Watchtower is a movie), the Resident Evil universe (through the six or so Resident Evil movies), the Lovecraft universe (through Lovecraft-inspired movies) and possibly The Purge (through the The Purge gauntlet and Horror Movie).
Recurring Characters
Separate to re-visiting settings, it is possible to encounter multiple copies of certain characters in different jumps.
For example some Dead or Alive characters can be found in Warriors Orochi; many Nintendo characters are found in their original jumps (eg: Super Mario) and again in Super Smash Brothers; Batman can be found in the DC jump, Young Justice, the Lego jump (The Lego Movie time option as well as Lego DC), and the Batman The Dark Knight Trilogy jump; Dante from DMC can also be encountered in Bayonetta, etc.
The characters are entirely separate - effectively different "clones" or alternate universe versions of each other. You could even have multiple copies of them as companions.