My top level computer folder for all theology matters is named "Theologos". Within that folder some 14,000+ files are organized into folders. Here is a pix of the folder structure within Theologos from a year or so ago (I fiddle with the structure from time to time):
http://gallery.myff.org/gallery/1499289/Theologos.jpg (there are sub folders within this structure, too)
I use a similar naming structure for book collections on my Kindle.
I use Dropbox, Google Drive, OneDrive, and Sugarsync for cloud based backup, sharing, etc. I backup locally to an external drive, SDCard (for use on my Chromebook Pixel), as well as an extra internal hard drive. One full hard drive image is made each day using ShadowProtect on an automated schedule. (I do consulting work for law firms and am quite paranoid about losing any work products.)
All files are sorted to be viewed by type as I usually know the type of the doc I am looking for: pdf, docx, txt...
When needed, I use X1 or DTSearch software for searching for files by content as they are more powerful than Windows search. Both are wonderful tools.
For theological research and study I use Logos Platinum (and online at biblia.com), SwordSearcher, and WordSearch (and online at mystudybible.com). (For those interested all TNARS faculty are eligible for faculty discounts at Logos.

) I also have the software version of the Puritan Hard Drive and download materials as I need them versus owning the external hard drive product. Many of these I convert to more readable MS Word or better formatted pdf formats using ABBY FineReader and then send to my Kindle.
One of my most valued items, one overlooked by the average user, is my set of browser bookmarks collected since the beginning of web browsers. I regularly export and backup these bookmarks (several thousand and counting). They are likewise organized along the lines of the folders shown above.