I had to make the same decision for my compositions few years ago. So, I started categorizing my compositions mainly on the Scientific classification theory, which means using naming convention according to that theory. Since I'd like to edit, copy-paste or transfer those scores online, at first I make a digital version (with Sibelius software) of my compositions. This would be very useful for future changes or other kind of manipulations plus the ability to make second backup of them for example on the online storage services; i.e. dropbox, googledocs, etc.
Then, according to that theory, I start naming (the folder of) my composition starting from the general category (genre) at the very left and trying to cover all the specification of that composition. for example:
Chamber music - Oboe solo and String quartet - After the rain - 2013
- The Chamber Music is genre,
- Oboe solo and String quartet is the general instrumentation for that piece,
- After the rain is the name of composition
- and the (optional) 2013 is the year of that composition.
(The year is not necessary since at the computer you can sort or find items by time, very easily)
In each folder I will put materials on sub-folders as full score, parts, audio, video, program notes,... (whatever applicable for that specific composition).
There is an extra benefit to make a digital copy out of your score (for example in Sibelius) that you can use “capture idea” menu. It's helpful if your composition is only few gestures, a beautiful melody or an interesting harmonic progression.
I also have found it quite useful to add unique number (at the end or just at the beginning) of the names, and that is something like the traditional opus number which facilitate remembering the hierarchy of your compositions as well as beautiful road-map of your career.
The hierarchy of biological classification (Example of scientific classification)