I write markdown files with Typora, backed up and synced with Resilio sync. I still use Evernote for clipping web sites. I'm working on a web clipper that saves directly to markdown so I can finally ditch Evernote.
Definitely a browser extension for clipping highlighted portions of websites and convenient browser integrations. I don't want to do the conversion to markdown in the extension itself because I also want to do some minimal processing, like download images so the resulting markdown file can be viewed offline. That requires either a desktop application or a service. I've been toying with the idea of integrating with dropbox, google drive, etc so you can choose which folder the markdown file and all supporting material will be saved to. Then you can read and edit the markdown with whatever editor you want. The clipping experience would appear to be entirely in the browser extension, just like with the evernote clipper.