The most neutral definition of a "well designed" website, without any further context, could be "created in a way that helps users achieve intended goals efficiently, while keeping max number of users happy about its look".
Again, different audiences will have very different answers. Here at HN, sites like https://www.mcmaster.com/ and https://www.craigslist.org win – because HN users appreciate old look and how efficient these sites are.
https://www.apple.com/ is an industry standard of a marketing site for consumer tech. It's not universally "well designed".
Other examples of well done marketing pages: https://www.sketch.com/ ; https://statamic.com/ ; https://linear.app/ got its share of hype recently.
Other times, a website is well designed because its content is awesome and is easy to consume. See https://ciechanow.ski/ and https://www.joshwcomeau.com/
Is https://github.com/ well designed? As an amateur developers, I'd say yes.
Is https://htmx.org/ well designed? Hmm, at a glance, there's no design at all. Is no design also design? That's a rabbit hole.
P.S. I often hear my website is well-designed :-)