Just want to give credit to the Zotero application that comes bundled in UberStudent.
I wrote a thesis of more than 300 pages and with several hundreds of references of all kind (books, research articles, manual added references, ...) without any problems using Zotero. Some of these references required individual citation style changes that Zotero also handled perfectly. I used the one-year-subscripton system provided by Zotero to work with references between 3 different computers (the lazy mode, instead of syncing hard-drives).
Don't fear using Zotero! It doesn't lack behind other reference managers (and I used a lot of them in a professional environment)
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