[1] He is known for developing average hamiltonian theory and using it to extend NMR spectroscopy, previously limited to liquids, to the solid state.

He is the author of ANTIOPE, a freeware general purpose Windows-based simulator of the spectra and dynamics of nuclear magnetic resonance (NMR).

[2] Waugh was awarded the Wolf Prize in Chemistry for 1983/84 with Herbert S. Gutowsky and Harden M. McConnell for their independent work on NMR spectroscopy.

[3] Waugh was cited for his "fundamental theoretical and experimental contributions to high resolution nuclear magnetic resonance spectroscopy in solids.

In the words of Ernest H. Cockrell, chair of the Welch Foundation, Waugh "discovered how to use NMR to study solids, creating a collection of tools that allows researchers to view the structures and properties of proteins, membranes, viruses, and many other critical components of life."