I haven't played the WAD itself and I haven't heard all the tracks yet, but I think my favourite so far is Mist at Dawn. I skipped ahead and listened to Weather Warning, but I have to say it didn't work for me and I was surprised by how popular it is.
I get that. Mist at Dawn is really good, but you have to put Weather Warning in its context. It accompanies the penultimate map (excluding the credits map), which is why there's a real weight to it. Those bells can sound really ominous.
If I had to choose my top 3 songs, it would probably be Alien Jungle (0:22), The Night Guard (32:06) and Weather Warning (1:51:21), but it's a tough choice. A lot of them are really good.
