Be sure that those games are in my heart too. But these numbers doesn't correspond to trully highly succesful games. That's why ID has been sold for only $100M. For a comparaison, Riot Games has been sold for $400M with only one game (League of Legend) [1].
Also, Minecraft[2] sold 7+ millions of java copies. It's more than x2 copies than Doom3 on "one platform".
Quake was/is one of the best games of it's genre, ever. It sold 1.7 million copies, as a shareware release.
Doom 3 sold 3.5 million copies. It wasn't a commercial success?
Not to mention the games that were built on top of id technology, games like Half Life, Call of Duty, et al