Another idea I had was to create a system of navigation based on seemingly random sequences of letters that previously were not indexed by search engines.

So your page could be the only one on the internet corresponding to "lzeinbt3mta".

It could be used to connect websites, which is something I have encountered before when content is duplicated across domains.

You could create a webring by having everyone include this term in one of their pages, this could potentially be griefed but I also think the standard search engine algorithm would help to protect it.

The terms would need to be distinct enough from other words so that you don't get search engines asking "Did you mean? X".

Limitations include people not wanting to allow search indexing (I have search indexing disabled for this blog), and web crawlers simply not indexing their pages (this might just not be a thing, I don't know).