For one, Ace Attorney 3's 300 joke ("This is madness!" "No, Maya, that is S. P. A. R. D. A.") was also a Devil May Cry joke. You know, Sparda?
Plus, the SFX for shock in Ace Attorney 2 is the exact same SFX they used for damage in the SNES Megaman X games
There's the "Excuuuuuuuuse me princess" joke, which is, indirectly, a reference to The Legend of Zelda
And I can recall a few more... just can't remember them right now