Find the orphans first
Take your full URL list — your sitemap is one — and your crawler's list of pages reachable by following links from the homepage. The difference is your orphan set. On most small sites it is bigger than the owner expects, and it is usually the pages added last.
Fix these before anything else. A page nothing links to cannot be improved into relevance.
Link from body text, not just navigation
A footer link tells a reader and a crawler almost nothing about what is on the other end. A sentence that links the words describing the thing tells them both exactly. Navigation is for structure; body links are for meaning.
Which means the anchor text matters: link the phrase someone would search for, not click here and not your bare URL.
Make it a step in publishing, not a project
The reason sites develop orphan pages is that linking is treated as a cleanup task. Two rules prevent it entirely.
- When you publish a page, link out from it to the pages it should reference. Easy, and everyone does this.
- When you publish a page, find every existing page that should now link to it, and add those links as part of publishing. Nobody does this, and it is the one that prevents orphans.
- Keep a hub page per topic that links to everything in that topic, so new pages have an obvious home.
- Check depth: if a page is more than three clicks from the homepage, something upstream needs a link.
What not to do
Do not build a block of fifty identical links at the bottom of every page. It is the oldest footprint there is, it dilutes everything, and readers scroll past it. A handful of relevant links inside real sentences outperforms it on every axis.
Do not link the same anchor text to two different pages. You are telling a crawler to choose, and it will choose the one you did not want.