My guess is that DOOM used a lot of public domain royalty free sounds from those CDs mentioned. They're just so prevalant. It's fairly obvious that this is a common practice in just about every genre of entertainment, especially movies.
For Quake 2 I believe id initially tried to do their own sounds (read this in some interview awhile back) while reusing some of the old Quake 1 sounds, but they eventually contracted it to Soundelux, a large commercial sound contractor. Soundelux was also on board for Quake 3 (The foley work in Q3's character sounds is surprisingly intricate.)
When compared to the sounds in modern games (MOHAA, SoF2, JK2, etc.), Reznor's work in Quake 1 lacks detail and authenticity. The sounds are relatively short, unrealistic, and don't have the intricacies and subtle nuances brought about by the now standard repertoire of piling tons of samples on top of each other to create a single sound (Raven does this a lot.)
What Quake 1's sounds do have are emotions and a theme. The ability of Reznor's sounds to express a feeling that goes beyond the actuality of the object creating the sound. It hits the listener on a hard, distinct personal level, immune to analytical criticisms. All the while retaining that dark, foreboding, "gets into your head" reality that only a musician of Reznor's particular idiosyncracies can effectively convey.
"Life is not about the second chances. It's about the little mouse, and his voyage to an exciting new land. That, my friend, is what life is." - Dad
"Nothing livens up a robotic hymn of doom more than an amazing pair of jugs." - Brak