How to reconcile citations?

Another reason to use a citation manager: If you publish your dissertation later as a book (or even separate chapters as journal articles) the publisher will require you to reformat the references into another style. This will be hell if you did them manually, and easy as pie if you used a reference manager. (My dissertation had 40 pages of references. Imagine doing those by hand!)

Well, http://www.zotero.org will automatically generate a bibliography for you based on the embedded citations in Word. It does import Endnote libraries, you can export your Mendeley library as bibtex and import that into Zotero. In any case, you'll need to invest the time into cleaning up your references for the final push.

Yeah, I can't imagine writing a dissertation without some kind of citation manager. My dissertation had almost 400 references, which is not atypical. Managing those manually sounds miserable. Word actually has a rudimentary reference manager built in now, but I don't know how good it is. The nice thing about using EndNote, etc. is that you don't have to have all of your citations figured out before you start writing. As you read or write, you come up with something you want to cite and enter it into EndNote. When you're ready to cite it, you paste a citation in. If you find a useful citation later, you enter it into EndNote then and paste in the citation. When you're ready to format, you can mess with the settings within EndNote until you have the complete bibliography formatted the way you need it. As cgk notes, Zotero can also handle this for you (as can Papers if you're a Mac person), and it's pretty easy to import libraries from one citation manager to another.

I really can't recommend Zotero as your citation manager enough. I went from reluctantly using it as my citation manager to now using it as my complete document database. I'd be lost without it. The learning curve is shallow. Download the standalone version and the Word plugin and you're off to the races. There's also a Firefox plugin to import citations from a webpage (like a PubMed journal page). Seriously, spending a couple hours figuring this out now will save you days down the line.

If you use LaTeX with BibTeX, it is automatic--sources which are referred to in your text are listed in the bibliography, all sources in your database are not listed. BibTeX is easy to use with most other citation database software, too, like Endnote and Mendeley. Otherwise, there isn't enough information given in this question--the citation manager you should use depends on which software you're using to write your dissertation.

Does the http://endnote.com/support/faqs/enw plugin (for Word, maybe similar software) work with your version of Endnote? Basically, when you want to insert a citation in your Word doc, you highlight the source in the Endnote program, switch to Word, and hit Alt+2. I just wrote a dissertation and highly recommend this.

Absolutely you should find some sort of plug-in system that works for you so you can embed the citations directly from your reference manager AS YOU WRITE. If you don't do that, you will be in for a horrible time at the end. If you decide not to do that, for whatever reason, you can at least write a script (or find someone who knows how to script) to do the bits of your process that involve extracting anything between parentheses and alphabetising them. If you use an open-source ref manager (maybe export from Endnote to Bibtex), you might even be able to script some sort of auto-generation of the final citations from that alphabetised document. But you'll have to manually clean it up before that stage, to remove any parenthesised material that isn't a citation. And instead of "find anything in parentheses" you can do a more complex find algorithm using regular expressions, which might help you eliminate some of the chaff. (And help you pick up the full citation in things like "Author (2012)". )

Yeah, EndNote or a similar reference manager is the way to go. I thought it was weird that my PI was so adamant about starting with EndNote as soon as I was writing my first piece as a second year, but he was totally right. I'd be curious as to why you don't have this type of software already? My department provided all students with a copy of EndNote for free....

I use a document/citation manager now (Sente), but I didn't for my dissertation, and it didn't kill me! But yes, if you're just starting the writing process, you'll be much happier if you choose a reference manager now and add stuff to it as you go.