The Main thing you want to look at, is the EASE of how you want to operate the system. Cobalt Machines are much easier to operate with control panels, security updates supported by the manufacturer, Special "ports" of other clients/servers (mysql, php etc). The one thing that the cobalt lacks in is the "perl" area. So if you are planning on running a very large amount of CGIs and you know your way around a Linux Server, then I would go with the INTEL server.
However if you are not sure how to work linux all that well , or don't know advanced administration techniques I recommend that you get the cobalt.
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