TV - Separate, Alpha by title.
Movies - Alpha by title, but series grouped together. Hobbit and LOTR are all in one group, for instance, under H. LOTR comes after Hobbit just like OT comes after PT.
Format - Mixed. Used to separate Blu at first but have so many of each now there’s not much point.
Criterion - I think I have one (Rushmore?) so not an issue.

Interesting thread idea, even if you didn’t ask first. 😉

JEDIT: You didn’t ask about fanedits. For replacements (like Matrix sequels) my favorite versions replace the original in the original case on the shelf. The original discs go in storage in a spindle. Other fanedits (like additional Matrix sequels that aren’t my favorite, or njvc’s Pulp Empire that can’t replace the original) go in a spindle but in an easily accessible location that isn’t the main movie/tv shelving.