Epitaph of Twilight (Novel, Unreleased)
AI Buster* (Novel)
Sign (Anime)
Zero (Novel, Unfinished and Untranslated)
Infection, Mutation, Outbreak, Quarantine (Both games and novels, has a non-canon alternate universe manga called XXXX)
Liminality (OVA series, happens at same time as the above entry)
Unison (Bonus Sign episode, might or might not be canon, we're not sure)
Legend of the Twilight or "Udeden" for short (Manga, has a non-canon anime alternate universe)
*The sequel, AI Buster 2, is a collection of short stories that happen all around the above timeline
Roots (Anime)
Cell (Novels, Untranslated, happens at same time as Roots)
Alcor (manga, Untranslated)
GU: Rebirth, Reminisce, Redemption (Games, have a manga, movie and novel version, all of which are non-canon alternate universes)
GnU (Manga, happens at the same time as above entry, may or may not be canon, we're not sure, Untranslated)
Returner (Bonus Roots Episode, this one we know is canon)
Link (Manga, currently in progress, Untranslated)