I'm going to write all interesting stuff which i found in game files:
That tool which Allison gave us is "Seeing Tool".
there's white drawing of a moustache (Propably can be found somewhere in-game with Seeing Tool).
There's a full rig of Chester from BINR.
That thing which chased Henry in a boat is simply "Giant Bendy hand"
The meatly easter egg is somewhere in the Administration (his room is in "Administration" folder)
In the ending room there are letters from Allison and Wally, they're mentioned as "Extra Props" so maybe they're a hidden easter eggs?
Theres an invisible white door outline somewhere in CH4 which can be seen with Seeing Tool.