It obviously wasn't the first note taking app, and it's very much not Free, but the nature of its linking sparked Obsidian and Logseq's growth. I've been a happy paid user since the early days.
The biggest reason I stick with it is that it supports both being E2E encrypted and synchronising, without me having to set anything up. I wouldn't mind running a server, but (unlike many in the comments) I actively don't want my tool to operate on a pile of Markdown documents on the filesystem: because then I need to worry about maintaining those files everywhere I want to access my notes. Roam will automagically drop an encrypted backup on my laptop every day, my regular backup system will take things from there. For day-to-day use, sync is per-block and effectively live.