There are about 50 of those scattered throughout the game.
Here is something I found pretty funny being a sailor.
These are manhole covers marked as Material Condition X-Ray, you will only find them on a U.S. Navy vessel, so I had to stop and chuckle when I saw them. Not really an easter egg but pretty interesting if you are familiar with shipboard closures!
What does material condition X-ray mean, though?
It means that every closure that is marked with an “X” must remained closed, or must be closed after going through or working in the space. It’s for very low traffic places like manholes into a ships smoke stack or any type of tanks (fuel for example). The three most common MATCONs are X-Ray, Yoke, and Zebra. Each setting gives a ship better damage control ability, X-Ray being the least, Zebra being the most. 
Maybe they are for the Borealis
Talk to the guard at the Sector B door in AM, he’ll say something funny relating to the administrator.
Also one of the scientists across where Gman is talking, on the computer, has some funny dialogue.
Heard one of the security guards say “say hi to dr. cross for me” refering to Gina Cross the HEV suit instructor lady.
Also if you sneak up on that lonely scientist in AM you can hear him fantisizing about Dr. Cross 
How about that guard in AM that refers to gordon’s diamond-cutting butt
I noticed that the Bullsquid tends to eat what kills and in the process the enemy corpse gets gibbed and gradually the gibs themselves gib until the Bullsquid is full.
One thing I miss is the HECU approaching your dead body (or other slain enemies) ensure that you are in fact dead.
Are there really no references to Aperture Science? Seems odd to not at least make one reference to them seeing as they were Black Mesa’s biggest competitor.
there is a warning sign that is similar to a Aperture one some were.
Here are mine:
I’m pretty observant when playing, and the HL series is pretty notable for lots of ‘easter egg’ typed additions to the game. This will add to the replay value I hope.
I took a few here. I’m sure there are many more, but I wanted to share these.
At the very first level after the calamity when 2 doctors get pulled into a vent there is a hovering limb that rotates and bleeds indefinitely. Go look. It’s early in the level.
Video here (right at the beginning): https://www.youtube.com/watch?v=GMof0tZefm4
The remains of some vortiguants after using the .50 cal. Can’t remember what level. I think it’s after using the artillery.
WD-40 is a really popular and really useful water displacement spray that is great for fixing well… anything. Black Mesa Source added a model of WD-43 which I thought is quite funny, seeing as it doesn’t exist. It’s a bit of an inside joke I guess. Can’t remember the level, but there are a few around apparently.
EDIT: Apparently it’s Einstein. There are no other copies of this photo anywhere. Can’t remember the level.
At the last level if you walk around the side doors on the left as you walk in and take a small path to a few other rooms with seemingly nothing in them, you get this message:
I have no idea what it means, but the translation seems to be something like this. (It is very hard to read no matter what resolution or graphics detail you play on):
[i]“This is some ignorant??? ???”
"Actually I just can’t think
of anything usable?? to say.
really. This??? I guess is my
fault. Everything is always
my fault after??? all.
288?? + 282…
252 - ???
252 - 181???
2548198???[/i]
EDIT: Someone else had a better picture of it.
Go check it out for yourself and see if you can translate it properly.
Please post your own if you found any!
Also here is a video I took of a bunch of glitches and other things I thought were funny. Not meaning to double post but yeah:
The assassins wear long-fall-boots. I choose to believe they’re Aperture brand.
Incidentally, I noticed houndeyes seem to avoid barnacles, which makes me think they have a symbiotic relationship with one another, where the houndeyes knock things into the barnacles with their sonic attack, and then they eat the partially digested bits the barnacles spit out (the houndeye’s beaks don’t look very strong, so they could use some help).
“Emergency shutdown, needs fixing as soon as possible.”
How short the game would have been.
The inbound times has a headline referring to them:
Also check out that “pizza-chart”.
“Report to super cool laser lab please.”
That line in Anom. Mats. cracked a smile.
Found this examining the sound script code. – The lines start at the top and are arranged from soundscapes_c0a0 and up.
There are a few awesome one-liners. lol
Oh my god, that’s hilarious.