I've been thinking about it, and Puzzle and Dragons, just as a game that exists, has crossed over with so many different media properties that it's hard for me to count.
Off the top of my head, crossovers they've had, in no particular order:
- Neon Genesis Evangelion
- Yu-Gi-Oh!
- Magic: the Gathering
- Angry Birds
- Clash of Clans
- Hello Kitty
- Taiko no Tatsujin
- Street Fighter
- King of Fighters
- Samurai Shodown
- Final Fantasy
- Dragon Quest
- One-punch Man
- Bleach
- Jujutsu Kaisen
- Detective Comics
- Slayers
- SMT: Persona
- Monster Hunter
- Demon Slayer
- Fullmetal Alchemist
- Hunter x Hunter
- Fate/whatever
- the monogatari series, don't remember which one it was
- Kamen Rider
- Ultraman
- Power Rangers
- Star Wars
- Prince of Tennis
- all of Gungho's other games
and several others I either forgot or didn't know about, this is some wild shit. Other crossovers wish they had this kind of range. You can have a team that has Seto Kaiba, C3PO, the red Power Ranger, Hello Kitty and Saitama and have a Rathalos as a helper.