Classicists tend to use the Chicago Manual of Style rules for citation, though that depends on what venue the work is intended for--publishers often have their own rules or variations on the standard. Turabian, a derivative of Chicago designed for undergraduate research, is also popular for less formal work.
Classical works are typically referred to by chapter and verse, like Scripture, rather than in conventional footnote/reference style.
Plato Protagoras 309c
Virgil Aeneid 2.250-252
Note: For more formal publication, and if it's relevant to your argument, specify the edition of the work you're using with a full reference/footnote the first time you use it.
List of standard abbreviations (Oxford Classical Dictionary)
Citation managers are software that seeks to automate the mechanical details of citation by capturing citation information while you work, and then producing footnotes/references and a bibliography for you later. Depending on your specific needs there are several which might be helpful. Short summary below; detailed description of your options on the Citing Sources research guide.
Endnote (get it): The only one of the big three which is not free to you. Windows/Mac software which you install on your computer. Designed to allow you to permanently maintain a large, complex collection of citations and the documents associated with them. Uses a format widely supported by library databases. (Tisch documentation)
Refworks (get it): A web-based approach to the problem, which means you have access to your citations on whatever computer you're working on--as long as it has an Internet connection. (Tisch documentation). Refworks format is widely used in library databases.
Zotero: A free plugin for the Firefox web browser which allows you to create your bibliography while you browse web-based resources. For resources it recognizes, Zotero short-circuits the export-then-import process usually required for Endnote and Refworks. (Zotero documentation). Current version includes the ability to share citation information online, which has traditionally been Refworks' main advantage. Zotero can read files in Endnote and Refworks format. My favorite of the three.
Citation styles from the University of Chicago Press. Used in history and political science and in other disciplines within the humanities and social sciences. Designed for students writing term papers, Turabian is a simplified version of The Chicago Manual of Style. Note: If you can't find a citation example in the Turabian manual, see Chicago.
Chicago and Turabian provide two style options:
Notes and Bibliography. Features: Uses footnotes, typically followed by a bibliography. Facilitates referencing of unusual source types. Used often in the humanities, history, and business. See the Chicago-Style Citation Quick Guide for many examples of footnotes in many formats.
Author-Date System. Features: In-text parenthetical citations of author(s) last name, publication year, and cited pages, followed by a reference. Used often in the sciences and social sciences.
The citation examples provided below are based on the Chicago Manual's 16th edition, published in 2010; the Chicago Q&A website provides additional information and clarifications.
Evernote allows you to keep track of a wide variety of information on the web: take notes, snapshots of web pages, save audio recordings of lecture notes. It also allows you to sync all of that information between the website, your PC or Mac, and almost all smartphones (including iPhones and iPod Touches).
Dropbox provides storage for files which you can then access from anywhere with a web connection. You can also install a program on your computer(s) so that you can just drag files into it and have them automatically sync to your other computers and/or phones. Free for up to 2 gigabytes of storage.
Google Docs (general version) (Tufts version) provides a word processor, spreadsheets, and presentation software you can use from anywhere with a web connection. Most importantly, it *automatically saves your document* as you work on it and keeps all of the previous versions. Also easy to publish a document for comments, or to let multiple authors work on one document.