If you take the box from Calhoun's locker into the firing range and shoot at it a plush toy of a Chumtoad will come out. A similar Easteregg happened in the original where if you shot the box in Calhoun's locker a living Chumtoad would come out.
In barney's locker there's a poster for a game called prax wars 2 Dante's revenge. The game was featured in the original blue shift as a arcade game and was named after a canceled game known as prax wars.
In the chapter captive freight the player kills a sniper with a tow launcher. Later in the chapter when escorting rosenberg you can find the remains of the same sniper.
At the end of the chapter captive freight in the prototype labs you can hear several old computers. The sound of these computers is actually of the original hl1 computers.