Bibliographies
The most general kind of reference is the bibliography, which is a list of documentary resources for your subject. A bibliography compiled by a specialist will typically filter out unreliable resources, although in that case there's the risk that it will 
also filter out views with which the specialist disagrees. A particularly useful kind of bibliography is the annotated bibliography, which comments on each item: usually it will give you an idea of why the item might be important for you to use.
The Internet has lots of bibliographies on early Christianity. Here are a few.
Resources for late antiquity. "Late antiquity" is roughly AD 300 to AD 600. This is on the server of the history department at Nipissing University and is somewhat maintained by Steven Muhlberger, a professor of history there.
Bibliographic information base in patristics. From l'université Laval, this allows the searching of 375 journals. It must be done in French.
Bibliographies for theology at Creighton University, a Jesuit school in Omaha, is sectioned into a number of areas, including early Christianity.
The Oxford bibliography of early Christianity (you'll need library credentials to access the whole of this) is part of a set of hundreds of Oxford bibliographies. They are available through academic libraries, including the University of Toronto Library (UTL). Each bibliography gives a concise introduction to the area and then lists dozens of selectively curated books and articles, with brief annotations. Each is written by an acknowledged expert in the field, and is peer-reviewed. The bibliography of early Christanity is by Eric Rebillard, a Sorbonne PhD who is a professor at Cornell University.
NOTE. Often in a google search you'll come across a resource that you can apparently access only by paying a fee — but it may well be available for free to UTL users. The complicated way to get this source is to open another browser window, go to the UTL catalogue, and search. The simple way is to use a handy bookmarklet, which you can download here. This sits in your browser bookmarks, and whenever you come to a resource that asks you to pay a fee, click on the bookmarklet to see if it's available free through UTL.
The Oxford Handbook of Early Christian Studies has four dozen articles on various topics by first-rate scholars.
The Yale Guide has a brief annotated bibliography of reference works, with links.
Primary source material
The distinction between primary and secondary sources is discussed on Course Webpage #2, and it can sometimes be nuanced or slippery, but in general a primary source in history comes from the period you're studying. A very large amount of Christian writings in the period to 843 are available online. Without a doubt, a much huger number of early Christian writings have disappeared: the ones that have survived have survived for a reason, often because at least one person in the intervening centuries decided that it should be preserved. Thus, some of the works that we have from antiquity are those that a monastic scribe or a librarian in medieval Ireland decided were important. Usually, of course, the works that have have come down to us were the works of well respected male leaders. As a result, most of the primary source material that we have today for early Christianity were written by (or were thought to be written by) bishops or other male leaders and teachers. (Later in this course we'll note a few exceptions: for example, some troves of very interesting uncurated material have turned up in the Egyptian desert.)
Ante-Nicene and Nicene Fathers (CCEL). These comprise three collections: the Ante-Nicene Fathers (Christian writers to C.E. 325) in ten volumes (one of them an index volume); the Nicene and Post-Nicene Fathers, first series, in fourteen volumes (all Augustine and Chrysostom); and the Nicene and Post-Nicene Fathers, second series, in fourteen volumes (from the Council of Nicea in 325 to the 600s). The translations were made between the 1860s and 1880s, and frequently feel rather stilted. These are all available at the Christian Classics Ethereal Library (CCEL), hosted at Calvin College.
The Ante-Nicene Fathers in ten volumes in an older translation (eds. Alexander Robertson and James Donaldson, T&T Clark, 1867 – 1885) is available from Wikisource. The edition used is apparently from a US company which pirated the original, in days before international copyrights were enforced.
The Nicene and Post-Nicene Fathers, series 1, from the same US publishing house as the Ante-Nicene Fathers volumes above, has fourteen volumes of Chrysostom and Augustine.
The Nicene and Post-Nicene Fathers, series 2, has fourteen volumes by various early Christian authors.
The Internet Ancient History Sourcebook includes primary source material, sometimes excerpted for school use, in several categories, including Christian origins and late antiquity. Later Christian sources are in the companion Internet Medieval Sourcebook. It was begun in 1996, by Paul Halsall, a then doctoral student in history at Fordham University, New York. It's still hosted at Fordham. The translations come from various sources, and are of varying quality.
The early medieval monasticism project lovingly curated by Albrecht Diem, who teaches history at Syracuse University, links to databases of early monastic archives all over the place.
Online Reference
Reference materials are particularly useful sources when you want an introductory overview of a subject. They are, of course, written by fallible people, and although they are often couched in a tone of authority and omniscience, they can never be assumed to be entirely dependable.
1. To look up the name of a person, place, event, theological idea, etc., you can use an online reference such as one of the following.
Wikipedia.
Launched in 2001, this is an online encyclopedia that can be edited by
anyone. It has millions of articles in several languages. In
theory, the open-collaboration concept ensures that entries will be
frequently updated, so that mistakes and bias can be corrected.
Articles are unsigned.
The Catholic Encyclopedia (1914). This compilation has some very good scholarship but takes a strictly pre-Vatican II Roman Catholic position on all matters.
The New Catholic Encyclopedia (NCE), 1967, 2nd ed. 2002; the link requires you to have UTL access. The NCE is a great resource; see the Wikipedia description of it.
St. Pachomius Library. This calls itself a first draft for a living encyclopedia of Orthodox Christianity. It identifies many people, giving an Eastern Orthodox opinion of them, and it includes texts as well.
2. For maps, online resources include:─
World history maps by Thomas Lessman (an amateur historian in Kansas).
A linked list of on-line atlases is supplied by Christos Nussli, a businessperson in Switzerland specializing in digital historical cartography, is a wonderful resource for maps of the various regions of the ancient world by date (380, 420, 460, 500, 540). For more maps, see Thomas Lessman's Atlas.
The textbook for the course
The textbook for the course which this website supports is Justo L. González, The Story of Christianity. González is retired, but among other things he has been a faculty member at the Interdenominational Theological Center in Atlanta, and is director of the
Hispanic Summer Program, Fund for Theological Education. He is also a minister in the United Methodist Church, U.S.A. In an article "Globalization in the Teaching of Church History", Theological Education 29 (spring 1993), 49–69, he writes:
"It was at Yale, mainly through contacts with Bainton and Latourette [Church history professors at Yale], that I began to realize that church history could be not only interesting, but even relevant. Yet, I still saw myself primarily as a historian of theology, with perhaps a side interest in the general field of church history. Since that time, I have had occasion to write through the history of the church three times....My third "go" at the history of Christianity was a series of ten small paperbacks, originally published in Spanish, then translated into Portuguese, and finally published in a two-volume English translation-adapation as The Story of Christianity. There, I tried to implement most of what I suggest here, while at the same time trying to provide a book that could serve as a basic text for courses in church history."
Other texts
The Cambridge history of Christianity includes volume 1, origins to Constantine; volume 2, Constantine to CE 600; and volume 3,, 600 to 1100. These date from about 2008.
Charles Freeman, an independent English scholar, published a well reviewed survey text in 2009, New History of Early Christianity.
Among older books, W.H.C. Frend's Rise of Christianity (1984) is a very thorough survey of over 1000 pages; Henry Chadwick's The Early Church wwas a staple volume for earlier generations of theological students and a model of balance and readability.
Online journals
A large number of journals are available online through www.library.utoronto.ca to those with University of Toronto library cards. A list of good scholarly peer-reviewed journals is available from Yale, here. The following are publicly available.
Bryn Mawr Classical Review This journal contains reviews of books in the classics, including works in early Christianity. It's published at Bryn Mawr College.