Academy of Champions: Soccer has Prince of Persia in it, along with characters like Rabbids/Rayman which cross over with Mario multiple times.
Genghis Khan is in AoE2, and also in Civilisation. Leonardo da Vinci is in Civilisation and Assassin's Creed. Ezio is in Soul Calibur, as is Link.
For Hitman, Agent 47 appeared in Lara Croft's Poker Party, which also had JC Denton in it. Deus Ex had a crossover with Final Fantasy, where characters from Mankind Divided appeared in Final Fantasy Brave Exvius. Cloud is in Smash.
Not got anything for Worms just yet. There are
these, but those seem to be just masks/items. Superfrog does appear in Worms though.
Morrigan from Dragon Age is in MySims SkyHeroes, which is the same universe as Sim City, which features Bowser.