Independent?

Everytime when we plan a holiday and we need a hotel we use more or less the same booking systems on the internet to find and book hotels. But I also wonder every time: how independent is this hotel booking system? Do hotels have to pay to be in the list? Do they have to pay to end up high in the list? It's not very clear to me and that makes that I usually also check if I can find the hotel in other booking systems, or even directly on the homepage of the hotel. Usually it's pointless, but we have had occasions where we found the hotel on different sites with different prices.