One example could be 'Katawa Shoujo'. It explores the lives of students with disabilities in a school setting. The characters are well - developed and it delves into their personal stories, relationships, and how they deal with the challenges in their lives.
Another one might be 'Clannad'. While not entirely centered around disabled students in a school, it does have characters with various personal issues that can be seen as a form of disability in a broader sense, like emotional and family - related challenges. It's a very emotional story that shows how the characters support each other and grow together.
There's also 'Planetarian: The Reverie of a Little Planet'. Although not strictly focused on a disabled school, it has elements that touch on themes of isolation and difference which can be related to the concept. It's a story about a post - apocalyptic world where a lonely robot in a broken - down planetarium meets a wandering scavenger.