There's only 2 known Easter Eggs in System Shock 2. Perhaps at a later date I may include stuff other than Easter Eggs on this page, but for now Easter Eggs are all that are here.
The Dancing Robot.
On the third year of your training, before you enter the room with your three choices for your next year's career, look through the glass to the room left of you. Inside is a robot dancing, of all things the macarena.
Psionic Monkeys: "Join Us!"
This is by far the more entertaining of the two Easter Eggs. In the introduction level to the game, where you choose the military path you want to take, there is a basketball on one of the pillars outside. After you get off the train, head up the grav lift and follow the street to the right. When you reach it's end, climb up the pillar to your right. There is a basketball at the top which you can pick up. Although you can't open your inventory, once you have it I'll be in your inventory until you reach the Vaun Braun. Once you're on the Vaun Braun, hold on to the basketball until you reach Deck 5, the Rec Deck. On this level is a basketball court. If you make a shot with the basketball, you'll get an e-mail consisting entirely of monkeys screeching and smashing things up. However, if you open it and read the text, you'll get an entirely different message.