Some examples from Namco X Capcom alone:
* the Soul Edge crosses dimensions by itself (justifying its own series' crossovers and functioning as a McGuffin), and is used to separate Darkstalkers' Morrigan and Lillith. whom in their own series essentially share a soul
* Dr Bomb from Bravoman works for Heihachi Mishima, and build Waya-Hime from his game based on the techniques of Taki from Soul Calibur
* Taizo Hori, whom you may know as Dig Dug, worked as a digger alongside Rockman Volnutt and Roll casket from the Megaman Legends series
* the concept of Namco's
United Galactic Space Force series actually got used and referenced in a game, as Hiromi Tengenji from Burning Force and female-protagonist-before-Samus-Aran Mausyo Tobi from Baraduke teamed up, initially on a mission to capture Tron Bonne.
* the fact that Masuyo and Taizo are divorced, as established in the Mr Driller games, is ackowledged and used
* in the posters for Captain Commando, it's mentioned that Sho/Ginsu practices Bushin-Ryu, the same art as Guy from Final Fight - the two of them are a team in that game, and Guy helps out in Captain Commando's team super, essentially expanding the version we see in the MvC games
* the Tower of Druaga appears right in the middle of the demon village (makaimura) from Ghouls and Ghosts
* Zouna's desert pyramid from the Legend of Valkyrie has a portal in its center that's used as one of the dimensional gateways in the game. It also contains a room where in its original game its robot mooks Robodians were built - in NxC it also builds Phobos bots from Darkstalkers, Prototype Jacks from Tekken, Waya-Hime copies and Kos-Mos copies
* Kazuya's devil gene is a considerable part of his and the broader story's involvement with the Tower of Druaga and Ghouls'n Ghosts villains
* the time travelling elements from Dino Crisis are used to connect characters from the past like the Soul Calibur cast, and future characters like the UGSF cast, Strider and Captain Commando
* Master Meioh from Strider really takes a fancy to the Gnosis from Xenosaga, and the copying abilities from the Doppel enemy from Captain Commando
* speaking of Strider, I liked how the Unknown Soldiers from Forgotten Worlds were introduced in the game by being interrogated by Ton Pooh from that game, which was a frustrating task for her as they have no actual names to give
* on the topic of Forgotten World, the fact that Sylphie's shop just pops out of the ground in the middle of the levels is a plot point - that thing can apparently also cross dimensions. Also, despite her constant smiling she's depicted as an incredibly greedy creature and her attacks reference a bunch of really old Capcom games - she's pretty much Capcom personified
* while the most famous Resident Evil characters were's present, the Dead Aim representatives were still in, opening the gates to stuff like zombifying a dino from Dino Crisis
* the Black Valkyrie from the Valkyrie series is depicted as having power over the dead, which opens the gates to bringing back character who are/were dead in their games' canon, like the first Armor King from Tekken
* Valkyrie herself is shown as working for Ishtar from the Tower of Druaga series. At one point Ishtar makes Heihachi Mishima deliver the Golden Seed from Legend of Valkyrie to Valkyrie, so she can release the previously mentioned dead characters from the control of the Black Valkyrie.
There's a lot more than these, but these stand out to me. Of course, invariably the original characters tend to dominate the wider plot, but I really liked with MonolithSoft achieved with that game story-wise.
PXZ flt more disjointed and individual characters and series felt less important in comparison, but
apparently there are people from the NxC team on board, and with a confirmed, "sequelable" success on their hands I think they have the tools to excel again.