One program that I have found to be indispensable, largely because I am so completely inept in creating a coherent filing system, is Copernic. It exists in a free version and a professional version, but I have found the free version to be sufficiently powerful to meet all my needs. It can be downloaded from this link. Upon download and installation, you can customize it by specifying which directories you want it to index, and specify what kinds of files it should retain in its indexes. I have mine set up for .doc and .pdf. Depending on the size of your desktop, it might take several hours for it to compile the initial index, but you can begin to use it right away, although the results will naturally be incomplete. Once it has been installed, however, and it has created the index, it subsequently updates that index in real time, meaning, as you create word files and pdf files, for example, the index is being updated to reflect the new documents. (I think it updates itself every 10 seconds.) Copernic is not only much faster than Google Desktop, it is also much more private insofar as it does not share the contents of your Desktop with Google’s servers, but rest assured, I’m sure the NSA has other ways to find out what you are reading :). It will also search your e-mails, and is much faster in that regard than Microsoft’s search tool in Outlook Express. It can also find deleted e-mails which may be useful at times even if you cannot recover the actual text.
I have installed Copernic, along with Dropbox, on all the computers I use, and the result is that I can usually find without much difficulty files that I prepared long ago or articles that I had downloaded and saved but forget where I saved them. The key is to begin saving all your research files and saved articles into your drop box, and then when you install Copernic, just have it index your Dropbox.