Things you may not have noticed (spoilers ahoy!)

[GhylTarvoke]

Please post your easy-to-miss observations here (not necessarily easter eggs)! I'll start.

Spoiler below!

1. In the beginning dream sequence, Ashley says that the red tracer fluid is green. This is a reference to the inverted spectrum thought experiment.

2. The tracer fluid's location changes with each playthrough - I think it's always in the last place you look, but I'm not certain. Anyway, it's a clever introduction to the game's mechanics.

3. If you type the code into the door at the PACE lab without looking at the book that contains the code, Simon says: “Wow, I guessed it! That's incredible!” (Credit to reddit.)

4. The game's ubiquitous brain image is on one of Munshi's computers. (Credit to my brother.)

5. It's possible to encounter the Construct by entering the room with the Omnitool too soon. Don't say I didn't warn you.

6. The first WAU flower is keeping someone alive, perhaps in a cortex chip. He begs you not to use the flower.

7. It's impossible to encounter the Construct in the vents, despite the noises and lights.

8. When escaping the Construct, you can either turn off the scalding steam or run right through it.

9. You can either use Amy's ID or Carl's ID on the computers.

10. In Upsilon's comm center, calling Theta gives the following message: "...there is something better here... it's here..." Calling Omicron gives the following message: "Kill yourself. There's nothing left to live for."

11. Have you seen the following creatures underwater?
Crab - everywhere.
Moray eel - near the trapped K8.
Shark - between Lambda and the CURIE.
Manta ray - at Delta.
Snail - at the floating spheres near Omicron.
Gulper eel - in the abyss, near the climber.
Shrimp - between Tau and Alpha.

12. There are two ways to enter the transit system: by freeing the K8, or by fiddling with a control panel.

13. In the shuttle, you can see slightly different videos by choosing different locations.

14. After the shuttle crash, if you forget the Omnitool and then go back for it, you have a super-cool encounter with a Flesher. (Credit to reddit.)

15. There's a sunken submarine called the Pequod.

16. If you get hurt by the Flesher at Lambda, the subsequent dialogue is slightly different.

17. If you enter the crashed shuttle before meeting Catherine, Simon mentions it while discussing the ARK.

18. If you sabotage the CURIE without talking to Catherine, she later freaks out. (Credit to reddit.)

19. At Delta, the eyeballs are surrounded by maggots. Gross.

20. Killing the K8 is very painful.

21. Outside Theta, there's an audio recording in which Sarah Lindwall gives Catherine some personal advice.

22. In Catherine's room, you can pick up various objects to ask Catherine about them (a robot teddy, a Chinese fan, a doll, a piece of the Vivarium, and a proto-ARK). She also becomes more annoyed the longer you stay.

23. At the end of Theta's residential hallway, there's a locked door. If you look through the window, you can barely glimpse an enemy (either Akers or a Proxy - I'm not sure which).

24. The unbroken chip containing ARK scans changes location with each playthrough.

25. You can place Brandon Wan in eight different scenarios (four possible environments, either with or without Alice). Simon gets more upset with each simulation.

26. Near the simulation room, there's a door that's initially closed, then partly open. You can hear a Proxy on the other side.

27. In the room at Theta where you can scan yourself, there's a WAU flower. If you use it, Catherine expresses disgust.

28. There are two ways to get Brandon's connector chip: either by smashing the window, or by unlocking the door.

29. It's possible to lock Akers in a room, but he eventually escapes (presumably through a vent).

30. Akers makes a final, brief appearance before you're flushed out of Theta.

31. The code to cancel Omicron's quarantine is randomly generated.

32. Some bodies in Omicron move around while you're away.

33. In Omicron's cleanroom, there's a control chip. If you take it to Catherine after applying the structure gel, she remarks that the gel on the chip isn't enough for the power suit.

34. Omicron's marine life laboratory has all three WAU Fish on display.

35. The climber dialogue changes slightly if you kill/spare Simon-2.

36. In the abyss, straying too far causes you to take damage from an unknown source, apparently a disembodied constellation of lights.

37. In the abyss, Johan Ross sometimes watches you from a distance.

38. It's possible to enter Ross' room at Tau.

39. You can either move the ARK around TAU by using the freight lift, or by crashing down the ladders.

40. The far end of the tunnel that you use to transport the ARK has collapsed. Under the rubble, there's a body you can datamine.

[felixmole]

Spoiler below!

• The robot head girl says things like "Away", "Don't come any closer", etc. as the player moves in her area.
  
• After entering Tau, you can hear "Caution, airlock pressurizing". When moving forward to the rooms located on the side further ahead, and then backtracking towards the entrance through the hallway, you can see the airlock door opening for Johan Ross.
  

[GhylTarvoke]

... okay, that's pretty cool.

I forgot some things about the K8, but #2 and #3 (below) may have been coincidences. They certainly seemed deliberate - can anyone confirm?

Spoiler below!

1. The K8 plays a little tune when it rescues you. I'm sure everyone noticed, but it was a great moment.
2. Soon after I freed it, the K8 stopped at a coral growth and shined its light on a small hole. When I looked closer, I saw a moray eel. I would have missed it otherwise.
3. At Delta, there's a station with broken K8s. As I poked around, the active K8 came over and nuzzled one of the broken ones. (Think WALL-E.) Then it came over and nuzzled me! Too cute.

[Potato]

Spoiler below!

1. In the beginning dream sequence, Ashley says that the red tracer fluid is green. This is a reference to the inverted spectrum thought experiment.

Pretty sure this is just in reference to the traffic light in the dream scenario you're. You can hear a bunch of cars honking and stuff right after she says it.

I always thought #6 was weird, the talking door in Upsilon. Never thought I'd feel weird about killing a metal door, but it was interesting. Cool list so far! A lot of these I encountered in my playthrough, but some of these are pretty neat.

[GhylTarvoke]

Oh, the traffic light didn't occur to me. That makes sense.

I keep finding stuff that I hadn't seen before. If you jump off the ledge at Delta, the K8 somehow saves you. That robot should have a fan thread or something.

[Romulator]

Spoiler below!

Construct's voice lines are rambles of various messages. Some contain rather threatening vulgar swearing, and sometimes it speaks in different languages.

Edit:

Spoiler below!

In Omicron, pouring the structure gel onto the rat causes it to twitch erratically, as if coming back to life.

[FlawlessHappiness]

Killing the K8 is very painful.

Funny, I didn't notice that.

[Mudbill]

Killing the K8 is very painful.

Funny, I didn't notice that.

You must have a heart of stone.

[DreadFox]

Spoiler below!

You can choose to keep Amy alive in the transit station, only unplug one of the sockets then go back to the switchboard, activating it will give the message "emergency power only". The shuttle will still crash, but it will give the error message "power unstable" as opposed to the track blockage message.

[FlawlessHappiness]

Killing the K8 is very painful.

Funny, I didn't notice that.

You must have a heart of stone.

Of course I noticed it
And since you're implying that it's not very hard to miss, it may not belong to the list...

Though it's an entertaining list. I like it, with those extra witty lines.