I know Brandon is already satisfied with the provided answers but I do think this is an interesting topic to discuss about regardless.
Personally I‘ve come to terms with the fact that no amount of categorization and effort I put in will ever be enough. At some point I realized I seem to find some new interesting game I had never heard about about every couple of days or so, and that’s not taking into account the constant flow of new things in the shape fan translations or the stuff that happened recently with the Atomiswave ports, which I always want to try. I think eventually you just gotta accept that, like it or not, trying to organize games is going to be a perpetual work in progress, just like @robinhoodie was pointing at.
Considering that complete romsets always feel overwhelming and give me a hard case of analysis paralysis and never actually playing anything, I have essentially opted for adding only games I feel like playing in that exact moment (it is always one or two very specific games what makes me want go through the whole process anyway), and games I feel like I may want to play on short to mid term, adding anything that shows up and seems interesting during the process. Doing this while being conscious of what I said about the endless nature of the whole process but also that moods and interests shift and change and what you felt like playing at that moment may not be what you feel like playing now has helped me a lot.
Coincidentally, this way of taking care of things also has the collateral benefit of producing a list a lot more concise, manageable and frankly, more interesting, because there is always some sort of ethereal idea on your mind that ends up shaping the whole selection, and it ends up being fun seeing after the fact what you had on your mind when you set it all up.
So TL;DR would be: abandon all archival hope of producing any list or system that feels "final", embrace the fact that you will want to tweak things down the road and put the focus on playing and actually putting the damn thing to use. Ironically enough, if you keep doing that, down the road you will end up with something that resembles an actual final list, if not on terms of the whole actual catalogs, at least on terms of what really appeals or speaks to you, which in the end is what anyone should care for.
And you don't have to fully commit to it either, as some people has already suggested, you can have either the complete romset on your PC, some sort of already curated pack as Smokemonster's, or your own custom system via an Excel file or whatever.
