My computer files are pretty organized (not so much for the paper) this is the method I use:
1. on my hard drive there is a folder for each surname
2. Within the surname folders are separate folders for each individual. I use the following naming convention: Last Name, First Name Middle (birth year-death year)
Example - Smith, John Joseph (1850-1926). This helps to differentiate between people with the name name
If its a female, it's Maiden Name, First Middle, Married Name (birth-death). Example, Jones, Mary Alice, Smith (1855-1900)
3. Within each of those individual's folder are scans of all documents, pictures - everything is scanned. The scanned files are named for the individual like so: Smith, John Joseph (1850-1926) - Census - 1930 US Census
it was an absolute pain in the rump to initially set up, but now there is no problem finding someone or knowing what file pertains to who. If a file pertains to more than 1 person a copy is in each person's folder on the hard drive.
Also, I have a Mac so for any file or folder you can right click and add notes about the file or folder - those notes are searchable so I use those extensively as well.