I've heard lots of recommendations as to how to sort your files. The bottom line is, that it has to be something that works for you...not someone else. You need to be able to find your files when you need them. This is how I sort mine...
Those "Tree" folders are broken down into surname folders. Then under each surname folder I break them down a bit more into specific records/events. There are folders for Birth, Census Records, Death, Education, Immigration & Naturalization, Marriage, Military, Newspaper, Pictures, Probate, Property, and Tombstones. Outside those folders I have miscellaneous items that don't really have a specific home. I could create a Misc folder, but as a matter of personal preference don't. I like seeing them floating around without a home so when I notice that I'm starting to acquire multiple records that can be grouped together I then create a new folder. If I created that "Misc Folder" I know myself and just wouldn't check it often enough to see if things were ready for a new grouping. Also in the free space I've got a surname "Research Log". When I conduct research on a specific surname, in the log it goes. It's also a great place for surname "To-Do" lists.
I use the PAF program for my family tree, but I have to admit that I'm eyeing the Legacy software after attending some of Legacy's webinars. I like what I'm seeing. I just haven't made the commitment yet. More research is needed to see how flawlessly my tree will transfer. Anyway, before I get distracted talking about a genealogical wish list...I was going to mention that in the PAF program I ensure that I've got people being assigned MRINs (Marriage Record Identification Numbers). I'm sure the majority of programs can assign MRINs.
What this means (if you didn't know) is that people are assigned a specific number when they get married. Documents in my binders are filed by Family Group Records and since the basis of those family groups are marriages, if someone got married their records go to that MRIN not under their parents. Since my binder filing system already does that, my digital system mirrors it. I don't place multiple copies under different surnames. They go with their married surname. So what do you do when you've got several marriages for an individual? Well, that's really up to you. I usually put them with the last marriage's MRIN, but you may have your own system.
The PAF program (and I'm sure most others as well) can print out a report that gives you the MRIN along with the couples they belong to. It makes a perfect index when you can't remember what someone's married name was. But I digress...that is more helpful with binder/paper files and that's another Sorting Saturday!