APA (American Psychological Association) style is commonly used in the social sciences. The APA released a 6th edition of their publication manual in 2010, which contains many updates from the previous edition.
MLA (Modern Language Association) style is commonly used in the liberal arts and humanties (ex. English). The MLA released a 7th edition of their publication manual in 2009, which contains many updates from the previous edition including new recommendations for citing online or born digitial sources.
The Chicago Manual of Style is an all-purpose, multi-discipline, general citation manual. The most up-to-date 16th edition was recently released in 2010.