A possibility largely neglected until very recently due to a variety of factors, timbral tuning is a system that takes into account the actual "real-world" overtone spectrum of any instrument or voice, be it real or virtual, and uses intervals between these overtones (and perhaps their multiples, quotients, inverses, etc) as a basis for tuning. This differs from just or rational intonation, in that JI only accepts integer relations and thus necessarily limits its purview to harmonic (or close-enough) timbres, while timbral tuning can also embrace inharmonic sounds of any stripe.
(Note that what exactly "close-enough" means is debatable, and one could make the argument that a subtle form of timbral tuning arises in several instruments which display inharmonicity, such as the stretched tuning of a piano or the balancing act across a guitar's neck.)
The resources of these kinds of tunings are theoretically as rich as those of JI. In practice, resources are limited by the number of identifiable overtones in the source timbre (plus the accuracy of their measure or definition), and it may not prove fruitful for very noisy or dense timbres that fail to give an impression of definite pitch, such as cymbals and flat gongs. Nevertheless, it may be far too early to make any definite judgements about so young a field, and it is undoubtedly ripe for exploration. An important pioneer in this field is Bill Sethares.
Works and Examples and Things