Author of some of the most complex tales of multispecies interaction, her 'central' universe contains the plotlines known as Alliance/Union, Cyteen, and Chanur within its multiple loci. The Alliance/Union series is an excellent beginning point, and includes the following books, in chronological order: ...did I miss any?
One of the most attractive characteristics of C.J.'s writing (I hope she won't mind my referring to her in that way for brevity) is its focus in most cases on the alienness of humans. I have read three of her major 'universe' arcs in their entirety - the above-listed Alliance/Union books as well as the Chanur stories and the two trilogies of the Foreigner series. The latter is her most recent of the three, and it shows.

While it doesn't rise above the other two in quality or in scale (indeed, compared to the others its scale is quite limited) it is probably the most political of the three. I say this not in the grand 'interspecies/intersystem' sense, but in the most personal sense. Her careful, almost obsessive attention not so much to detail but to completeness and consistency produces a two-species relationship (humans and the atevi) which is more complicated than any relationship she has introduced thus far. One reason for this is that it is almost entirely face-to-face, as both races are confined (initially) to a single planet, whereas her other stories treat worlds and stations as single players.

In any case, back to my main point about humans as aliens. Even in the Alliance/Union universe, humans are aliens on every world we see. We never see Earth, other than as a distant sort of concept, even on those books set within the Solar System. Most of the books depict humans inhabiting artificial environments or worlds which aren't theirs by birth. Despite this, however, the politics of this series are all intrahuman, with the possible exception of the azi and the slight intrusion of the Downers.

Chanur is all about the complex interactions of multiple species in a tenuous and shifting Compact, into which the potental addition of humanity is dropped to stir and shatter alliances and alignments. In those books, humanity never manages a full speaking part; the sole human with such is limited by a language barrier to a pidgen and the ever-so-subtle interpretations of motives, actions and behavior.

This is why I read Cherryh's science fiction - she has the rare ability to create not only races which look and act differently, but truly think differently. In so doing, coupled with her storytelling, I am able with no trouble at all to feel their confusion, fear, anger and wonder when presented with 'merely' human behavior with which I myself have no trouble identifying.