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Look for the Lambda sign (the half-life symbol) this is a clue to some hidden goodies.
Also look out for the G-man, you will see him from time to time on your journey.
Model animation behavior
Whenever there is a breencast up, turn on console and sv_cheats 1, then noclip and find a box that when noclipped into, has a dr breen half body (probably referring to Half-Life). This is not referring to Half-Life, the game itself, but this is how the model animations occur in that game. Its a way of making the model size smaller, and so there are two models for Dr Breen, one is him standing and the other is him having the animations in this half-body. This is done for other models, too.
Discarded audio file
If you Quicksave when you're going to jump onto the train, but then load, you will see a discarded sound called "A hint made by valve". It isn't discarded in this case because it is in Nova Prospekt, but it is hard to hear (its combined with wall ambient sounds).