Short answer: The clearnet is pages that search engines crawl. The deep web is content behind login or paywall — banking, mail, intranet. “Dark web” means services on overlay networks such as Tor, typically with .onion. The layers are technical, not moral.
Clearnet
Public websites with ordinary domain names. Google can find them. HTTPS protects the content, not the fact that you visit the page.
Deep web
Most of the internet: accounts, records, internal tools. Not “dark,” just not indexed. A patient portal is deep web and legal.
Dark web / overlay
An onion service is not reachable through ordinary DNS resolution. It lives on the Tor network. That says nothing about the content. Media, whistleblowing (SecureDrop), and documentation use the same protocol as dubious services.
What the terms do not do
They do not replace a threat model. Equating “dark web” with crime confuses transport with the act. If you want a link list, this is the wrong page — see Links.