I have actually been in environments akin to most of Black Mesa. Usually, it is neutral with no overwhelming odor. At times, there are scents of steam treated with volatile chemicals. Some areas will reek of chlorine, but hopefully they receive the necessary amount of ventilation.
Musty corners exist as well, with a tinge of mildew. It is very hard to smell grease, but grease is used everywhere, so there’s always a hint of it (if your nose is sensitive enough). Depending on how close you are to an air-vent, you may pick up other scents, like dust on warm electronics (fan motors, etc.).
Surrounding the cafeteria, you get a lunch-room smell that has dug itself into the walls with forty years of cooking oil and some accidental fires staining the walls with a tinge of smoke. Don’t get me started about areas that allow smoking… they smell like ash on a New Jersey beach.
Anywhere frogs can access will smell like pond-water, especially where it grows stagnant. I have the hydroelectric dam (and areas downstream of it) in mind.
Coffee will show up wherever it is being brewed, as well as desk-like offices. To a lesser-extent, carbonic acid may also be detected wherever soft-drinks are popular. Only in gyms and locker-room areas do cologne and spray-deodorants stand out, unless you are in a hallway or stairwell where somebody walks by with way too much cologne on.
Black Mesa should have a gym, now that I think about it. I suppose the facility is so large that we never had an excuse to pass through it. It smells like your usual gym, with cheesy sweat in the ceiling tiles and industrial carpets [if installed].
Right now, though, I am struggling to find a description for the scent at work that has been following my clothing home. I would describe it as crusty cheese. I have yet to determine the origin of it. I first noticed it in force while standing in the bathroom, so I have very negative associations with it, despite it showing up elsewhere.