I have tried almost every note taking app out there, and none of them is perfect. I do not want to go into too much detail reviewing them, but I eventually settled on OneNote.
The more I use it, the more I notice its strengths. I created a template that brings together my daily, weekly and long term to do lists, along with all my notes, in one place. The infinite canvas is a big advantage for me. It handles PDFs well, external links smoothly, and more importantly for you internal links too. You can see my template below.
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It has a decent web clipper, syncs reliably across devices, and it is free. One of the most important things for me is that it is cross platform, which means I can use it on my work PC, personal Mac, iPhone and iPad.
The only caveat is that handwriting to text conversion works only on PC. Still, it covers more than 80% of what I need, and given my experience with note taking apps, that is a win. It became almost my second brain.