What are the salient differences between the Pāḷi Nikāyas & Chinese Āgamas?
I'm looking specifically for a comprehensive list of discourses that are unique in the Āgama collection and differences between parallel discourses.
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Venerable Analayo through the University of Hamburg has given online courses in 2012 and 2013 comparing MN suttas and MA sutras. So far not the whole collection has been covered but in the material covered in those courses, as I can recall, there are some minor differences here and there but nothing that would put in question the central teachings as we know better from the Pali Canon. In 2014 there was a course about bhikkhunis, and maybe next year there will be another course about MN/MA.
You may also want to check http://suttacentral.net/.
I'm not sure if this helps, but since you asked for a list of discourses:
There is an appendix at the end of "Buddhist Religions" (5th Ed.) by Robinson, Johnson, and Thanissaro, entitled "An Overview of the Three Major Canons", which lists the Pail Tipitaka, the Chinese canon, and the (or a) Tibetan canon. It's just lists though -- no commentary or comparison.
From my very limited exposure to Agamas, mostly Samyukta Agama (equivalent of Samyutta Nikaya):
For example, consider the following passage of Kaccayanagotta Sutta / Katyayana Gotra Sutra:
But when one sees the origination of the world as it actually is with right discernment, 'non-existence' with reference to the world does not occur to one. When one sees the cessation of the world as it actually is with right discernment, 'existence' with reference to the world does not occur to one.
'Everything exists': That is one extreme. 'Everything doesn't exist': That is a second extreme. Avoiding these two extremes, the Tathagata teaches the Dhamma via the middle:
From ignorance as a requisite condition come fabrications. From fabrications as a requisite condition comes consciousness. From consciousness as a requisite condition comes name-&-form. From name-&-form as a requisite condition come the six sense media. From the six sense media as a requisite condition comes contact. From contact as a requisite condition comes feeling. From feeling as a requisite condition comes craving. From craving as a requisite condition comes clinging/sustenance. From clinging/sustenance as a requisite condition comes becoming. From becoming as a requisite condition comes birth. From birth as a requisite condition, then aging & death, sorrow, lamentation, pain, distress, & despair come into play. Such is the origination of this entire mass of stress & suffering. Now from the remainderless fading & cessation of that very ignorance comes the cessation of fabrications. From the cessation of fabrications comes the cessation of consciousness. From the cessation of consciousness comes the cessation of name-&-form. From the cessation of name-&-form comes the cessation of the six sense media. From the cessation of the six sense media comes the cessation of contact. From the cessation of contact comes the cessation of feeling. From the cessation of feeling comes the cessation of craving. From the cessation of craving comes the cessation of clinging/sustenance. From the cessation of clinging/sustenance comes the cessation of becoming. From the cessation of becoming comes the cessation of birth. From the cessation of birth, then aging & death, sorrow, lamentation, pain, distress, & despair all cease. Such is the cessation of this entire mass of stress & suffering.
One who sees arising in the world, is not one who holds to its non-existence. One who sees extinction in the world, is not one who holds to its existence.
This is spoken of as ‘freedom from the Two Extremes,’ which is called the Middle Way:
That is, that "this existence" is the cause of "that existence", and "this arising" is the cause of "that arising". These are caused by ignorance, including even the entire arising of the pure mass of suffering. When ignorance ends, then from this comes the end of such actions, including even the end of the pure mass of suffering.”
To me it looks like (Samyukta) Agama sutras are closer to what the original sutras must have been (minus the lossy nature of Chinese language) - while Pali Nikaya suttas have evidently underwent editing and elaboration/formalization which often caused a loss of context-specific subtleties.
The bottom line is, if one wants to get a deep understanding of a topic, it would be a good idea to study the both sources. But if I can boil down the salient differences to a single point, Agamas seem to better convey the overall meaning of each discourse, while Nikayas are better at details.
According to scientists (can't find the reference now), the Sarvastivada Canon that later got translated to Chinese as Agamas, has been put in writing several centuries before the Pali Canon, which would make it that much closer to what was said in that First Buddhist Council. I wish we had Samyukta Agama survive in Sanskrit - it would be the best of both worlds.