I just read that Creepypasta Fallout 3 Conspiracy story on GNR becoming a Numbers Station and it got me thinking, how cool a feature that would have been?
Finding the small Bombshelter signals was one of the few things in F3 that really sold the world to me. I was SO creeped out when trying to locate the shelters, just listening to that Morse-code and in those two instances, the Farther pleading for help and then the Ghouls, talking. A serious mixture of sadness and being freaked out got me really into them.

But back to business.
Imo, the whole Numbers Stations concept could have been an awesome (Unmarked?) quest. Running around trying to solve a mystery of a signal (that was NOT a distress signal) which Pre-dated the great war and was still very much active. And not just a small 'seach and find' quest, but a big recurrence, happening throughout the game. Kinda like a Hidden Secondary Main-Quest that could drastically change the outcome of the main quest?

Heh, got a little carried away there.
Just thinking that, this is a thing that would have been fun to explore, since the only real 'Pre-war covert military operations' stuff you incounter is from the Chinese Sub-Marines (?) you find.