One of my most vivid recollections of the research project actually belongs to someone else's past. The first week I was in grad school, my advisor showed me a 15-year-old collection of filed and labeled index cards, index cards that were the organizing principle behind her dissertation. My version of that index-card collection is a database, complete with a custom front-end Web application, which I use in combination with Zotero to organize my research.
Stage in my thought process: Two (Information Processing)
Where I use it: Storing, cataloging, and retrieving notes for use in studying, researching, teaching and footnoting. Secondary storage of secondary scholarly sources in Zotero, mostly for the bibliography formatting. Long-term storage and organization of notes [exported from and originally taken in Skim](http://www.kalanicraig.com/2010/01/reading-and-annotating-skim/).
What goes in it: Processed information applicable to academic research or pedagogy. That includes my own annotations and responses to the entirety of a source, along with annotations and responses to specific pages or sections of sources. These annotations are tagged by source, category and keyword, and the annotations on specific sections of sources also include page numbers for reference and recall purposes. I also collect lecture and discussion plans (with dates instead of page numbers) and notes that are geared toward future projects but based in already-read sources. I also include HTML-formatted Chicago-style citations for each source exported from Zotero.
Why I chose it: For me to feel as though I'm properly attending to my research and teaching goals, I need a system that organizes and tracks my thoughts within each project as well as pointing out the common threads between projects. My custom app does this with tags (like Evernote and Zotero), with citations (like EndNote and Zotero), and with parent-child relationships between notes (like Zotero). This system serves as a long-term storage and retrieval solution for all of the research and pedagogy information gathering. It ties together all of the information about all of my projects exported from Evernote and Skim via tags, but it also acts as a bibliography and citation tool in combination with Zotero.
Check out a sample of one of the "Tag" pages, with links to related sources, related in-source notes, and related tags:
Zotero and EndNote played a very important role in the development of this system. I've used both. I hated EndNote because it was miserable at importing and formatting citations, didn't allow page-by-page note-taking, and crashed Word too often. I liked Zotero, but it didn't fit my needs in quite the right ways. I couldn't annotate my longer sources--primary or secondary, monograph or article--in enough detail or enough depth in Zotero. Zotero has gotten better at that, but it's still too difficult to tie a single note about page 56 of a particular book to that book's bibliographical listing in Zotero. I also had difficulty importing my annotations from Skim in ways that were useful for me. Finally, I wanted to be able to note-surf by using a list of related tags and related sources that were linked based on how often two tags applied to the same sources and to notes within those sources.
There are downsides to building your own tools, however. Zotero's bibliographic formatting and ability to store PDFs in full is a big plus. EndNote's integration with Word, however unstable, is a lovely idea. Combining custom code with Zotero was the key to a system that both tracks citations and allows me to properly organize my thoughts for research projects (though I still have to take the citations out of my system and put them into footnote form manually). Zotero holds the original documents and citation formats, my own programming keeps track of my responses to those documents on a page-by-page basis and ties the whole organizational system together.