On the computer, each surname has a numbered folder that corresponds to the Ahnentafel on the Home page. Each ancestor with that same surname has a numbered subfolder within that folder. Records (images and sources / citations) are saved within subfolders and are named starting with the numeric year, month, and date so that everything for that person is kept in chronological order.
In my office, each surname has a labeled one-inch binder that corresponds to the Ahnentafel on the Home page. Each ancestor with that same surname is kept in generation order within that binder. Generations are separated by a yellow piece of paper. Individual reports, family group sheets, and printouts or copies of documents and photos are kept in chronological order. Children are kept with the father's section, and their sections are set off by red, green, blue, or orange pieces of paper, which helps me to immediately see to which main line they belong (Roth, Evans, Dugan, or Bowman). Additional binders are added as needed. For example, the first few of my family binders are labeled:
1. Roth (A)
1. Roth (B)
3. Dugan / Bocook (A)
5. Evans (A)
5. Evans (B)
Each binder (with the exception of the first, which can start with a man or woman) starts off with a section for a woman when her maiden name is introduced into the family, and followed by all the preceding generations of men with that surname. Marriage records always stay with the woman, as they provide proof of name changes.
I use Family Tree Maker to organize the individuals in my family tree, and often attach documents or images to the person or facts for that person within Family Tree Maker. The drag and drop feature makes this extremely easy to do within the program, but I make sure to save a copy to my hard drive and print it out for my binders, as well.
While I had an online tree at Ancestry in the past, I was spending more time fixing errors and syncing issues than I was researching. It has proven to be more effective (and less stressful) to use Family Tree Maker and Ancestry separately, or by selectively attaching records from Ancestry within Family Tree Maker, checking for errors as I go.
In addition to the digital copy on my hard drive, the hard copy in my binders, the copy in my Family Tree Maker program, and the backup copies of everything that I keep on my Western Digital My Passport backup drive and the online backup on IDrive, I also keep copies of everything in Evernote. When working with clients, I can give them access to their notebook and they can follow my progress and enjoy discoveries almost as quickly as I find them. They can even add things they find, such as letters and photos.
Skitch is the program I use for screenshots and annotating documents and images; it coordinates with Evernote, allowing me to save things directly to Evernote or to my hard drive (or both). Talk about a great tool!
I keep hanging files in a small file cabinet by my desk for general genealogy files and information about geographic regions. I tend to keep information about repositories (libraries, courthouses, etc.) in Evernote so I can access it from anywhere.
Original documents are NOT kept with the binder system described above. I make copies of them and then keep the originals in their own legal-sized binder within legal-sized, acid-free page protectors. This binder is kept in a safety deposit box as many of the documents are irreplaceable.