The "MATSim Book" is now the authoritative reference. The book is diveded into four parts, covering a broad range of topics.
There is an extract of the first couple of chapters, which contains the most relevant topics for new users:
(If the above link seems not to work, try to right-click the link and select "Save Link As…" or "Download Linked File As…" or similar, depending on your browser.)
It is planned that this book extract will be updated once a year to stay consistent with the code.
In addition to the book (and its extract), we've collected some topics coming up often below.