Chicago Manual of Style (notes/bibliography) is the standard for Art History. You can use its footnotes to comment on your sources or to insert information that would otherwise break the flow of your essay.
Zotero is a citation manager that easily captures citation information from library catalogs and article databases. It downloads PDF's as well. Has tagging and folder functions so you can organize all your sources. Integrates with Microsoft Word and OpenOffice to generate correct bibliographies, footnotes (even with ibid.!), and in-text citations.
ZoteroBib is a web based citation generator. It's easy to use and more reliable than other generators. Great if you don't need the functionality of a full-on citation manager.
Zotero addon that can automatically rename PDFs and store them in your preferred location. Extract PDF annotations and highlights in Zotero and turn them into notes.
