Citation managers are softwares you can use to store citation information, pdfs and research notes. You can then use them to create formatted bibliographies as you write your paper.
The Library supports Endnote, Endnote Web (online version) and Zotero with workshops and guides to each tool.
Some Citation Managers offer pdf annotation capabilities as well.
Zotpad for Zotero: Use with an IPad reader. Works with annotation tools.
Other Annotation Tools