I will talk about Pāḷi Nikāyas only because I never memorize Agama of the others.

For me, this is one biggest difference which causes many other difference between Nikaya and Agama.

Pāḷi Nikāyas have the rules of the keeper which we still follow on the rules through 2500+ years. In tipitaka and commentary tradition, since mahākhandhaka of vinaya mahāvagga is completed authored by upāli in 1st saṇgāyanā, all layman's teachers must have all of these qualities, which concluded by upāli in bhikkhunovādakasikkhāpada's commentary (which I translate below as follows):

Qualities of nissayamuccaka-bhikkhu (teaching lay people)

1. Proficient to recite pāṭimokkha-pāli and to understand it's commentary.
2. Proficient to recite and to understand 4 bhāṇavāra (~1,000 syllable) of sutta and their commentary, to teach laymen on uposatha day.
3. Proficient to recite and to understand sutta for bhikkhu's life such as andhakavindasutta, mahālahulovādasutta, ambaṭṭhasutta, etc.
4. Proficient to recite and to understand sutta for teaching in 3 chances: banquet for saṅgha by layman (nidhikaṇdasutta), funeral ceremony (tirokuṭṭasutta), and auspicious ceremony (maṅgalasutta).
5. Enough understand to judge/to decide about saṇgha's ceremony such as uposatha, pavāraṇā, etc.
6. Proficient to recite and to understand his kammaṭṭhānā throughout the nibbāna-course.
7. 5 years experience in monk hood as a monk.

Qualities of bhikkuparisūpaṭṭhāpaka-bhikkhu (teaching bikkhus)

If above layman's teachers want to teach bhikkhus (ūpajjhā-ācāriya, nissaya-ācāriya), they must increase their skill level to all of the following qualities.

These are for abhivinaya teaching:

1. Proficient to recite mahāvibhagha and bhikkhunivibhaṅga (first 3 books of thai 45 books pali-tipitaka) of vinaya-pitaka-pali. At least, he can relay with the other 3 bhikkhu. Proficient to understand it's commentary, too.
2. Proficient to recite all saṇgha's ceremony in vinaya-pitaka mahāvagga and julavagga.
3. Proficient to recite 14 vatta in vattakhandhaka.

These are for abhidhamma (kammaṭṭhāna) teaching:

4. Proficient to recite one of this suttanta-pali: mūlapaṇṇassa (1st/3 parts of M.N.) for student in M.N. faculty, mahāvagga (2nd/3 parts of D.N.) for student in D.N. faculty, sagāthavagga+nidānavagga+khandhavāravagga of S.N. or mahāvagga of S.N. for student in S.N. faculty, before half of A.N. or after half of A.N. or ekakanipāta+dukanipāta of A.N. for student in A.N. faculty, jātaka+commentary (because kammaṭṭhāna was described in commentary) for student in jātaka faculty.

Qualities of bhikkunovdaka-bhikkhu (teaching bhikkunīs)

If above layman's teachers want to teach bhikkhunī, they must increase their skill level to all of these qualities:

1. Proficient to recite whole tipitaka-pali and commentary-pali. Or at least, he still must recite whole tipitaka, but he can recite just one commentary of suttanta, first 4 parts of commentary of 7 parts of abhidhamma. However, vinaya-commentary is what he must recite it all.

Reference: tipitaka and commentary of vinaya pācittiyakaṇḍa bhikkhunovādakasikkhāpada and vinaya mahāvagga mahākhandhaka.

TL;DR

The summary from the following book is that:

• Oral transmission of the Early Buddhist Texts (EBTs) were very reliable in different schools.
• Even if there is difference in content between the Nikaya and Agama versions, they are all doctrinally identical.
• There is a very high degree of correspondence between the Nikaya and Agama versions of Majjhima Nikaya, Samyutta Nikaya and Digha Nikaya.
• All texts which are almost word-for-word identical between the different versions, although in different languages, were authored before the Sthaviravada-Mahasanghika split.
• Anguttara Nikaya and Ekottara Agama are structurally identical but have significant content differences. The Ekottara Agama is said to be unfinished and contains proto-Mahayanist additions.
• Other EBTs which are part of Khuddaka Nikaya have a common core, but the contents can be quite different, between different schools.
• The Abhidharmas are even more divergent between the different schools.

Details

From The Authenticity of the Early Buddhist Texts by Bhikkhu Sujato and Bhikkhu Brahmali:

We possess EBTs from a substantial variety of ancient Indian Buddhist schools, including the Mahāvihāra (modern-day Theravāda) of Sri Lanka, the Dharmaguptaka, Mahāsāṅghika, Mahīśāsaka, Mūlasarvāstivāda, Sarvāstivāda, and others of uncertain affiliation. A century of detailed study has consistently shown that they are essentially identical in doctrine irrespective of transmission lineage.

With corresponding footnote:

The only complete set of EBTs is the Pali version of the Mahāvihāra. Of the other schools we possess EBTs in a variety of degrees of completion, from a majority of the texts of the Sarvāstivāda, to only a few scattered Suttas and the Vinaya of the Mahāsāṅghika. In the case of the Mahāsāṅghika, this would change significantly if it can be established that the Ekottara-āgama in Chinese translation (T 125) belongs to this school.

The great Belgian scholar Étienne Lamotte says (in Lamotte, Étienne. History of Indian Buddhism: From the Origins to the Śaka Era. Publications de l’Institut orientaliste de Louvain. Université catholique de Louvain, Institut orientaliste, 1988): “However, with the exceptions of the Mahāyānist interpolations in the Ekottara, which are easily discernible, the variations in question [across the lines of transmission] affect hardly anything except the method of expression or the arrangement of the subjects. The doctrinal basis common to the Āgamas and Nikāyas is remarkably uniform.” This is in stark contrast to non-EBT texts.

... In 1882 Beal described detailed correspondences between Suttas in Chinese and Pali (in Beal, Samuel. Abstract of Four Lectures On Buddhist Literature in China. Biblio-Life, 2010.). He accurately predicted that “when the Vinaya and Āgama collections are thoroughly examined, I can have little doubt we shall find most if not all the Pali Suttas in Chinese form.”

.... Recently, in his detailed and thorough Comparative Study of the Majjhima Nikāya, Anālayo shows that all significant aspects of early Buddhist doctrine are the same across all extant textual transmissions of the Suttas of the Majjhima Nikāya (in Analayo. A Comparative Study of the Majjhima-nikāya. Dharma Drum Academic Publisher, 2011). Among the parallels to the Suttas of the Pali Majjhima Nikāya, the most important textual source, due to its completeness, is the Sarvāstivādin Madhyama Āgama preserved in Chinese. The Sarvāstivāda and Theravāda lineages must have separated approximately at the time of the Asokan missionary activities. This means that these texts have been transmitted separately for almost 2,300 years, including a period of separate oral transmission that lasted several centuries. And yet the doctrinal content is for all intents and purposes identical. This shows how conservative and careful the individual schools were in preserving the EBTs.

Moreover, this conservatism must have been inherited from the more unified—both geographically and doctrinally—form of Buddhism that existed prior to Asoka. There is no reason to imagine that the separate schools would all be conservative in preserving their canonical texts unless they had been conservative prior to their separation. Since comparative studies show that the core doctrinal material of the EBTs has been reliably transmitted for almost 2,300 years, the reasonable inference is that it was reliably transmitted also in the first 150–200 years of Buddhist history.

In addition to the full scale study of the Majjhima Nikāya, there have been multiple smaller studies of various parts of the EBTs. These have confirmed that all the EBTs share a similar level of agreement to what we find between the Suttas of the Majjhima Nikāya and its parallels. Such studies have been carried out for substantial portions of the Saṁyutta Nikāya/Saṁyukta Āgamas (in Bingenheimer, Marcus, trans. A Digital Comparative Edition and Partial Translation of the Shorter Chinese Saṁyukta Āgama (T.100). 2011 and in Choong, Mun-keat. The Fundamental Teachings of Early Buddhism: A Comparative Study Based on the Sūtrāṅga Portion of the Pali Saṁyutta-Nikāya and the Chinese Saṁyuktāgama. Harrassowitz, 2000), and to a lesser extent for the Dīgha Nikāya.

Caution needs to be exercised, however, regarding the Ekottara Āgama, which is nominally the collection corresponding to the Pali Aṅguttara Nikāya. Although it shares some significant structural features with the Aṅguttara, the content is often very different. The text is highly erratic and internally inconsistent, possibly being an unfinished draft. Scholars agree that it includes proto-Mahāyānist additions (in Lamotte above and also in Warder below), thereby establishing its late date of completion compared to the rest of the EBTs.

This high degree of correspondence among the EBTs across different lines of transmission does not exist for any other texts of the vast Buddhist corpus. Even in the stylistically oldest part of the Khuddaka Nikāya, such as the Sutta Nipāta, the Udāna, and the Dhammapada, there is substantial divergence between the schools. This is despite the fact that these texts do have a common core, which is found across the different traditions. With texts such as the Abhidhamma, despite a small common core, the divergence is even greater. But the vast majority of Buddhist texts are exclusive to the individual schools and do not have any parallels at all.

And also:

..... The first doctrinal split in the Buddhist monastic community was that between the Sthaviras and the Mahāsāṅghikas. Because this was the first split, some scholars, such as Edward Conze and A. K. Warder, have suggested that material that is common to both these groups of schools be regarded as the most authentic.

With corresponding footnote:

See Conze’s Thirty Years of Buddhist Studies, p. 9: “Where we find passages in which these two texts, the one in Pali and other in Sanskrit, agree almost word by word, we can assume that they belong to a time antedating the separation of the two schools [Sthaviravādas and Mahāsāṅghikas] , which took place during Asoka’s rule. ... This approach cannot, however, get us beyond 340 BCE with the Sūtra texts, because their Mahāsāṅghika version is lost.” And Warder says “... the agreement of these two schools [Sthaviravādas and Mahāsāṅghikas] should establish the oldest available textual tradition ...” (in Warder, A.K. Indian Buddhism. Buddhism Series. Motilal Banarsidass, 2000).

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 somewhat limited exposure to Agamas, mostly Samyukta Agama (equivalent of Samyutta Nikaya):

• Because Chinese is a much more ambiguous language than Pali, Agama translations to English are necessarily more "lossy" than translations from Pali, which preserves many subtleties inherent in Pali grammar. This makes Pali sutras more expressive at micro level.
• Agama sutras (at least those in Samyukta Agama) that have direct Pali counterparts, seem to be less stereotyped than their Pali versions. Meaning, a section that in Pali would often look like a stereotyped rendition of a matrika that repeats verbatim in many suttas, in Agama sutras seems to be in its pithy form. This makes Agamas more expressive at macro level.

For example, consider the following passage of Kaccayanagotta Sutta / Katyayana Gotra Sutra:

Pali

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.

Agama

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 survived in Gandhari - it would have been the best of both worlds.

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/.