(Spoiler potentially?) One that I know of is that in the "One Day Left..." portion of the Hikikomori Route, the rooms from Black Space are hidden in different parts of the map and can be interacted with once before disappearing.
The Easter egg where if you keep interacting with any mirror in headspace enough times, you get a small Jumpscare. You’ll know it happens when, wherever you are, the mirror background changes to vast forest.
This is a playlist with quite a few videos showing off different secrets and easter eggs. some of these are just jumpscares you encounter on normal routes though
in the Dungeon on the Sweetheart castle, if you're on the Omori Route and in the one day left if you keep interacting with the telescope that are in the last cell on the right, after a while interacting you finally can see the vision, that when you stop looking through the telescope you teleport to the cloud walway on black space 2 :D
theres a lot of references to the number "143" (if ur not sure what the significance of that number is, its basically just the amount of letters in each word of "i love you") but one that i remember the most is in the tree stump area of blackspace, when u go over to the edge after getting 'something' to follow u around, after waiting for 143 seconds ur able to then jump off of then edge. i forget what happens after that but im pretty sure u just respawn in the main blackspace area