SO, at first I actually just used folders, one folder -> unpacked games, until my library got too big.
Then I found xLibrary, which up to a certain version was almost perfect, neat design, convenient to use along with a browser plugin that let me browse game sites and save them to my library with just one click. Versioning, tags, info on available updates, pure gold. But, as I said before, 'up to a certain version,' the app got a redesign, and while it still looked decent and everything seemed okay, they probably added some support for managing the library with local AI, but the real nail in the coffin is a critical bug that can just delete your entire library from the app overnight. Problems with account connection, shitty backup system (doesn't really work).
Later on, in between, there were a bunch of other apps I tried: Playnite, F95Checker, wLib (Linux), and a few others I can't remember right now. But with each one, I ran into some problem, either visually or functionally.
At the end of the day, I found Atlas, which has its own game browser. You browse, click install, and if it finds a supported link, it downloads by itself, and you get to choose what format you want to install it in. You can automatically save, for example, in a format like D:/NSFW/{game_name}/{version}/{files}.
You can save and run different versions of the same game, and even automatically replace the old version with the new one when updating. The only downside is that when downloading multiple games, the download speed is limited, capping at 1MB/s.