When I was working on a ThM thesis at Regent College in Vancouver, B.C., I remember being frustrated as I attempted to keep track of the notes that I was taking for my research. It was then that I came across a powerful software program called Note Bene, which helped me when I began my PhD program.
Note Bene allows you to take notes on manuscripts, articles, books, and such that you are reading for your research and then formats these according to your specifications (MLA, APA, Chicago Manual, etc.). If you hate the tedious work of inputting footnotes in the right order, and in the proper format, you will appreciate Note Bene. It also will run searches using key words. So, if you can't remember what book or article you took notes on that relates to the Scottish Enlightenment and Adam Smith, for example, you can easily run a search to find the exact reference that you had in mind.
I now have over 1,400 entries on Note Bene. Although I admit that it is an expensive program, Note Bene has saved me hours of time over the past few years.