The Other Marty: The game's original premise had the hero as a tattooed, muscle-bound shaman versed in the ancient arts. When Clive Barker came aboard, the first thing he had the development team do was overhaul the hero into Irish paranormal investigator Patrick Galloway, wisely deciding that an everyman hero would work much better for the story (not to mention the Author Appeal factor). The hero's original design didn't go to waste, however: he can be seen as the Trsanti shaman wielding the Gel'ziabar Stone in the flashback cutscene.
Eight different spells were cut out. The game was even supposed to have three selection wheels: one for weapons, another for offensive spells, and another for defensive spells.
Mindshatter: disorients (it's the spell used by the Sil Lith in Oneiros).
Powerword: scribes a rune on the air and damages anyone on sight (used by the Veragos in Oneiros).
Ward: organic mines (used by Bethany).
Firefly: makes enemies glow, allows spells to seek enemies.
Shala's Vortex: originally supposed to protect from magical damage, before it was merged with the shield spell (which was initially supposed to protect only from physical damage).
Phoenix: initially a spell, not a weapon (used by Keisinger). Dynamite was supposed to be the missing weapon.
Phase: invisibility (used by the Drinen in Eternal Autumn).
Incantation of Silence: mutes sound.
At early stages of the development, the game was supposed to be called "Strange Aeons" (a H.P. Lovecraft reference) or "Siog" (a Celtic word for "Spirit World").
A cut level would have featured an Irish village overrun by Trsanti.
The gameplay would have been much less linear, and have more freeroam.
A dropped Scrye event was supposed to show Bethany coming back after being killed by Keisinger and banishing Keisinger to Oneiros.
Some items were also dropped. The wizard eye, for example, was like a surveillance camera that could put anywhere, but was dropped along with the multiplayer mode (being pretty much useless in single player). One can still be found in the Debug Room, though.