My most important contribution to music theory has been "All-Scalar Set Theory," which is a re-application of established combinatorial principles to xenharmonic ideas. My music theory tends to deal with xenharmonics because it's such an under-explored area, as well as rich with explanatory and aesthetic power. It's difficult to use a lot of tunings in your music if you play a fixed-pitch instrument, so I like to think that eventually Western music might adopt a small group of "favorite" tunings, or at least teach about one or two non-12-equal tunings in standard classroom curriculum. Thus, the goal of much of my music theory videos and principles is to make things easier for standard musicians to understand (which usually leads to a discussion of equal temperament, and/or major and minor triad comparison). I also create software to aid with this using Max/MSP, found on the "Software" page. There's nothing wrong with constantly comparing things to 12-equal, as long as it (a) helps understanding (b) we are self-aware enough to know that small differences do matter in tuning and chord progressions, and (c) that xenharmonic categories are legitimate "slots" or ways to think all by themselves, like 12-equal can be.
Scales and chord progressions from microtonal tuning systems.
A theory aiming to enumerate scales by their intervallic steps, instead of their pitch classes.
Analysis of highly non-12 equal pieces' harmonic and melodic content, of various genres and styles
Videos of lectures that I have given at various academic conferences around the United States.
Link to "Xenharmonics, Aesthetics, and Composition" when it is finished.
A video series with animated visuals, which, like Max/MSP, helps musicians to get the core concepts.
A video series about standard-staff methods of xenharmonic notation, mostly in equal temperaments.