I'm using PPR for domain rankings, but it's a very weak factor. It mostly affects the physical ordering on the results in the index, and given that queries have a timeout they'll execute for, it makes it so that higher ranking results are discovered first. Though in general, as I mentioned, this is a weak effect.

Explore2 and the website discovery tools now built into the search engine are using cosine similarity of the incident link vectors. I wrote a blog post about the technique called "Creepy Website Similarity" available :-) https://www.marginalia.nu/log/69-creepy-website-similarity/