There's no one particular way to keep your digital genealogical research organized but I thought I'd mention how I do it. If you have an alternative method please share it in the comments section.
My research is organized within a series of folders on my computer, two of which are named Family Members (Maternal) and Family Members (Paternal) respectively.
Inside these folders, I have a sub-folder for each person in my tree for whom I have documents, photographs, or both. I name them using the surname first, in capitals, then the Christian names and lastly, in brackets, a married name for women. In the case of several individuals bearing the same name, I add the birth year or other fact in brackets to differentiate. Here are some examples...
FRYER Richard (b abt. 1663)
PARKER Sarah Albinia (Dando)
TOYSOM Alexander (the elder)
WALKER Sarah (Dando, Hamilton)
!UNKNOWN Hannah (Pitcher) (b abt. 1808)
I use the exclamation mark before those with unknown surnames so these individuals will be placed at the beginning of the folder when alphabetically sorted.
I make sure my folder is sorted on 'name' so I'll be able to find my chosen individual quickly. To do this in Windows, you need to open up either the Family Members (Maternal) or Family Members (Paternal) folder and in the menu, choose View > Arrange Icons By > Name. If they are sorted Z-A perform this action once more and you should have them arranged A-Z.
Inside the person's folder, I create another folder named 'Documents'. This is where I store all the downloaded documents and scanned images of documents in my possession. Wherever possible, I date them so these documents will appear in order inside the folder. For example...
1869 - England & Wales, FreeBMD Birth Index, 1837-1915 - Alfred Charles Hibbitt.jpg
1869 - England & Wales, FreeBMD Birth Index, 1837-1915 - Alfred Charles Hibbitt.mht
1871 - England Census - Alfred C Hibbitt.jpg
1871 - England Census - Alfred C Hibbitt.mht
1928 - Alfred Charles Hibbitt - Death Certificate.jpg
1882 - 17 Feb - London Gazette - Bankruptcy of William Elbert Dando.pdf
1915 - Post Office London Directory (Part 5 - Law, Court & Parlaiment Directories) - William Elbert Dando.jpg
There is inevitably, a certain amount of duplication for instance, a census document might contain a family of 6 people so the same document will eventually be stored in 6 different folders. I feel this is the best way to ensure I'll always find the document I'm looking for but it does, however, take up more disk space.
Besides the 'Documents' folder, I sometimes create a folder called 'Photos' within the individual person's named folder. As the name suggests it's where I place photographs relevant to the person if I have them. These might include scanned pictures of the person or photographs of places where they lived or worked or churches where they were baptized, married or buried, either taken recently or from old photos. I might also include pictures of memorabilia such as medals or other personal possessions.
Whatever your method, remember to always back up your important data either onto an external hard drive or to CD or DVD or memory stick or to an online backup service, anywhere just so long as you keep an additional copy. Your data represents many hours of hard work which you'd be heartbroken to lose.