This list is in no way complete and is based on numerous reports gathered from interviews, articles and first-hand accounts from people close to Kubrick. So while we may never know for sure all the films he considered his favorites, this list is a pretty good start. The first 10 are an actual top ten that Kubrick submitted to Cinema magazine in 1963, this is the only known list that he ever officially put forward. After that, the films are categorized alphabetically by the director. Films starting from 94 have been added after the initial list, details below.
Added The Jerk, Napoleon and Ivan the Terrible - 09/2021
Added All That Jazz, The Bridge on the River Kwai and Summer of 42 - 09/2022
Added Funeral Parade of Roses - 12/2022
We are at 100 films now and I think I will be capping the list here. No more additions. Enjoy!