A "Bible" for molecular orbital theory? Linus Pauling wrote the famous "Nature of the Chemical Bond" which is a Bible of sorts for valence bond theory. 

However, VB theory was combined with crystal field theory to form molecular orbital theory, which eventually was condensed into the Hartree–Fock method.

Are there any "Bible" type reference books for these other methods?
I think an excellent book for understanding molecular orbital theory from a qualitative basis is Orbital Interactions in Chemistry by Albright, Burdett, and Whangbo. It covers a wide range of topics from molecules to solids.

The book doesn't go into particular methods, but instead illustrates how various MO treatments can understand a great deal of chemistry.