From the base game's soundtrack,
Water Caves has a special effect on me. Its mysterious hums and distant echoing horns seem to foreshadow how deep the world truly goes and how much there still is to be discovered. For me, the song's identity is tied with Mordre's quote about the world becoming more dangerous the deeper you go. Even when my character is fully souped up and nothing in the Lower Caves poses a threat anymore, hearing this song still makes me wonder about the real extents of UnderRail's universe.
Also, if you've never listened to Water Caves near a pond at night, I highly recommend it.
Second favorite from the base game would have to be
Deep Caverns. The background notes contrast beautifully with the low, drawn-out, isolating tones that make up the majority of the song. Without words it's able to tell you, "You're all alone. Terrible things have happened here. This is the end of the world." The song elevates Hollow Earth into something that evokes real emotion from me every time I'm there.
Personally, I think Deep Caverns is sadder than Scientific. While Scientific definitely highlights the tragic failures of academics trying to make UnderRail a more civilized place, Deep Caverns captures a much more personal tragedy. It gives me chills thinking about Dude's lost love interest, and how, when you call him by his real name, all he can muster the strength to say is "Why do bad things happen to good people, man?" Or how Gunter Vasilica, one of the researchers who had a sense of humor, was left to rot as a mutie in Caerus Residential for hundreds of years. Or how the one dying Apex Technocrat sees the writing on the wall heralding Biocorp's demise, and Ezra isn't able to comprehend his cynical world view.
Six's words as you hear Deep Caverns for the first time are prophetic:
"Hollow Earth. Your kin built it in ages which came before, but their own foolishness also razed it."