We have been considering all these questions lately prior to a change of hosting company.
The red/blue example you give I think is really an example of a "subdomain" with a different domain name. The server sets them up as subdomains (usually blue.red.com but you can allocate a domain name to each sometimes).However most often you will still end up with the same IP
One solution which we are thinking about is to find a host who will allocate different IP's for each domain, even though they are on the one account. There are very few that do this, but some do!
Even though the exact SEO advantage of having diff IP's for sites that interlink is not really known, it seems everyone agrees, that it IS a good thing, tho opionions vary from "some advantage" to "absolutely essential".
Google guy has said that domains in the same class C are still seen as separate, and even if the host says they can set up dedciated IP's for each domain, they will probably still be in the same Class C. (Assumption!) But according to GG, no problem for Google at least.
The best solution it seems is to have all your domains on different servers, and even different hosts, but if you have ever changing sites like us, it means lots of times in logging out of one host and into another, and they will probably each have their own intricacies that you will have to remember, and of course you will (like us) maybe end up paying for 100 to 300 MG of space for a 5MG site..
At the moment finding a host who can give dedicated IP's to each domain seems to us the best option.
We are NOT authorities on this, but this is the result so far of evaluating server moves options. I would be grateful if anyone can say whether we are right or wrong and add any intelligence to our research so far!