Woot, I finally made a Lemmy account so I can finally respond to this post!
I use a spreadsheet. Yep, a boring old spreadsheet, but it gives me the latitude to include whatever metadata I want, in pretty much any text format I want. I can say what my progress is in the game, and do so however I want. I can indicate what franchise it's from, including any numbering. I can modify game names to suit my own preferences and needs. I can say where the save files are located. I can say what platforms they're on (so I can include PICO-8 just for fun). I can indicate when I last backed up the game. And I can also search this metadata and filter and sort by it.
I used to use Backloggery to catalog my games. However, I sorta stopped after a while, partly because it didn't quite fit exactly how I wanted to catalog things, and partly because taking a break from it meant that I had accumulated a bunch more games.
That said, Backloggery has one major advantage over some other sites I've seen: the ability to enter whatever game name you want. This means I can catalogue any way I want -- including all manner of obscure indie games as well as romhacks and mods. I have a lot of very obscure games. Like, there's a fangame that has the main characters from an anime fighting each other like Mega Man robot masters. It's not the most interesting game in the world, but I've played it, so it's going in the catalogue. Oh, and when it comes to mods, I can decide whether they warrant a separate entry, too. Same with alternate releases -- I get to decide whether they're different enough to count as different games.
This can be a double-edged sword, as you can't quite connect fellow players of a game when you just let them say whatever games they want. But I've honestly never really cared that much about the oft-vaunted social features of game platforms.