Probably prioritises them very low, so they do not rock up in a lot of searches. Maybe puts them on the old server in the corner of the room.

There is a website that lets you search minus the million most popular websites, and it is very different.

Not a good analogy. Google isn't tacitly endorsing those websites. It is endorsing things in its store, at least to the level of "we think it's worth taking the vig for this".