Joplin: don't like the preview pane being split from the input. Workflowy: still use it as an outliner (for rationalising thoughts), it doesn't support inline images but with some help images can be attached to the description. Exporting made all the images available online without login! Love the look of the notes, and input is great. 
Dropbox Paper: lack of import options and export is single pdfs only. EverNote: no official linux client, £5 a month. Anything based on and markdown files: My notes require illustrations and these tools cannot add inline images / paste a - screenshot into the editor. Google Docs: I avoid the Google ecosystem for privacy reasons, plus compared to Dropbox Paper the experience is worse. OneNote: No cross platform native clients, don't like the free form placement on mobile. 
Input and search is ideal, grouping is ok (subfolders, manual tagging) I'm now happy to use my phone to look up notes when using Linux. However due to the number of people using it there are ways.
Apple Notes: export options are shit (tip: use AppleScript) no Linux client. Export option that retains text formatting. Capture webpages or supports pasting in part of webpages, that can be updated (not just a study tool). Supports images (copy paste and by upload). Cross platform native client (macOS and iOS, Linux and web optional). 
Minimal effect required to input, grouping and search notes. Ideally it will have a Linux version in the future. It allows you to tag and search is instant. Notes are just plain text but you can drag images into it which are then inserted using markdown. The default storage location is iCloud but it's easily changed to any location. IA Writer: Always thought this was a creative writing tool but it also shines as a markdown based notetaker. September 2020: I currently use Apple Notes with Workflowy, but switching to iA Writer. 
I work with the Apple ecosystem with a fallback Linux laptop. I'm always looking for a cross platform good value note taking solution.
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