I probably go overboard in how I handle my computer files but I've found this works best for me. I store everything by person as opposed to topics like census.
On my hard drive I have a folder called GENEALOGY and within that folder are subfolders for all the surnames in my tree named in this manner:
Surname, First Name Middle Name (birth year-death year). So for Ludwig Radwick his folder would be:
Genealogy>Radwick>Radwick, Ludwig August (1881-1951)
If its for a married woman I use this naming convention
Surname, First Name Middle Name, Married Name (birth-death) so for Ludwig's wife her folder would be:
Genealogy>Steinnagel, Amanda Edith, Radwick (1883-1949)
This helps to separate out people with the same name.
Within those subfolders I keep all the documents relevant to that person and use the same naming convention.
So the 1930 census for Ludwig or his death certificate would be in his subfolder and named like this:
Radwick, Ludwig August (1881-1951) - Census - 1930 (US).jpg
Radwick, Ludwig August (1881-1951) - Death - Death Certificate.jpg
Doing it this way allows me to sort the files by name and then all the census records get shown in order, death related items are lumped together, etc.
If something like a census record is relevant to more than one person then a copy is placed in each persons subfolder and placed in their name.
Same with pictures - if there is a picture of Ludwig and Amanda they each get a copy of it in their subfolder.
While it was a lot of work to set up initially, now when I look at anyone's subtolder I know it stands alone and has everything that is relevant to that person.
I also took the time to throw a little text document into everyone's subfolder which explains their link to me. Telling me someone is my 9th cousin 700 times removed doesnt tell me what I want to know.
An example would be something like "Bernard was the son of Joseph who was the brother of Adam who was the father of Lucy who was my mother."
When I print eveything out, each person gets their own binder with all of their information. This allows me to take one every now and then and read through it like a book of that persons life.
To the person reading this it probably sounds like I'm an escapee of some sort but once it's setup, it's really easy to maintain and nothing gets lost. And because there are multiple copies of common documents like census records or pictures, my number of backup files is increased exponentially.