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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!
I think for Kg2rg's current situation, I'd want to know how close the topics are that is being considered for a separate domain. I'd also want to know the history of /blue. Is it a new topic, or is this an already established subsite with link pop already built?
I've got the exact same situation I stumbled into yet again. Over on searchengineworld, I have the Opera subsite /opera that is now out performing the main site. I'm between a rock an a hard spot. I've got great linkpop built up and good rankings. Do I move it and take a year to recover? Or do I just leave it? For now, I'm just leaving it.
Thanks guys. Always great points of view here, as usual.