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I am using Joplin for years and I am pretty satisfied with it. (This is not a comparison because I have never used Obsidian)

It is doing 99% of what I ever wanted to do with my knowledge base. Though, if I am in a hurry and I want to quickly write something down (like a quick todo or something), then I am still using google keep, because editing markdown in the Joplin mobile app and waiting for it to sync, it is ok but not as quick as google keep. (I will not be surprised if there is a solution to this and I am doing something wrong)

Sure. There are plenty of alternatives, and being open source has its negative and positive things.

Self host is a good alternative if you want to play some and want to own your data 100% and I have tried to self-host Nextcloud on a Raspberry Pi once, but I gave up after some troubleshooting when I found that Hetzner offers ready-made Nextcloud boxes with https and all. I then synchronize my encrypted notes through Nextcloud pretty easily. I have never tried the Joplin cloud solution that was created after I chose Nextcloud (as an alternative also to Dropbox).

For me the best methodology can be abstracted to the following 3 things and in the end of the day is all I really need:

    1. Ability for a tree-like organization of notes. It can be as simple as some directories in your OS with text files and subdirectories. Or a cool app with Notebooks and Sub-notebooks etc. It doesn't matter.

    2. Ability to search everything at once. It can be a grep command or a an app with text search functionality. It doesn't matter again. Strive to have easily searchable titles and content in the notes (What "easily" means here, depends on your search preferences and habits).

    3. Ability to effortlessly synchronize your notes to different hosts. Maybe you'll put your simple directories and subdirectories of text files in Dropbox or something. Maybe you'll use a paid or open-source application with a mobile app or a web client etc.

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I explain the thought process here https://news.ycombinator.com/item?id=31799695 but it isn't important as those basic rules above.