One title that immediately springs to mind is 'Mirai Nikki' (Future Diary), though it's not the central theme. There's a character, Reisuke Houjou, a child with a twisted sense of love, who carries a 'baby' in his stomach—a bomb. It's more metaphorical than literal, but it plays with the idea of male pregnancy in a dark, psychological way. The series is a wild ride of survival games and twisted relationships, and this subplot adds to its unsettling vibe.
Another example is 'Tokyo Godfathers,' a film by Satoshi Kon. While not about male pregnancy per se, it features a transgender woman who emotionally 'gives birth' to a newfound purpose when she and her companions find an abandoned baby on Christmas Eve. The themes of unconventional parenthood and rebirth resonate in unexpected ways. If you're looking for something more literal, 'Akira' has a infamous body horror scene where Tetsuo's body mutates uncontrollably, including grotesque growths that could be interpreted as a nightmarish take on the concept. These examples show how anime often uses male pregnancy as a metaphor for transformation, trauma, or societal pressure rather than a straightforward narrative device.