So I own a dedicated server but don't have all my "affiliate" and blog sites all on their own unique IP. What are your thoughts? Do you put all sites on their own unique IP or share them?
No, I just have my big sites on their own IP, but my smaller sites or even customer sites share the same IP.
In most cases, it's a wastage of IP space if you have a separate IP for each website. I have had up to 20 websites on the same one. You can even use a reverse proxy behind 1 IP, serving multiple servers hosting your sites. Really big sites may span across multiple IPs. That helps to both distribute your load as well as provide redundancy.
Sometimes - I do it for the sites I think will make it big. No point wasting the world IPs on useless sites.