Over many years of collecting exonumia, I've "organized" my holdings in many ways: location, era, theme, metal, size, maker, etc. As my collection of counterstamped coins grew into the hundreds, I was faced with finding a logical means of organizing them. Alphabetically organizing them, made sense, but then too, there were ones that had no letters but had numbers, pictorials, symbols and the like. I found myself shuffling them about in the binder pages; this, in order to insert new additions.
I bought my first computer back in the early nineties and quickly discovered that a simple database was the answer to organizing the counterstamp collection. I created fields that addressed various aspects of the specimens; principally, the characteristics of the counterstamp and the host coin description. I added a memo field to write what I learned about each issuer or potential issuer. There are fields for catalog info, provenance, occupation, town, state, etc., etc. Thus, with a few, simple clicks, I can organize mini collections, locate and build upon what I know, what I have.
When it comes to locating a particular counterstamp for renewed study, the host coins/tokens are arranged by country, then denomination, then year in binder pages. A quick scan of a few pages in the appropriate binder is all it takes ...
Getting back to the OP's question, I've found that a database can be a great way to organize one's exonumia collection. Many pieces have cross-over appeal, and the database can visibly reflect that. For example, a Civil War token from a saloon or one with an error can easily be included in mini collections as such.