Andrea - very true and excellent comment about the subdomains being a part of the content pot but full domains obviously not, just like subdomains.
But here's the idea - if you have domains that have separate value by themselves, you use them as domains and link your sites in the menu. Subdomains are only useful for nice looking organization if you don't use/need SEO. So let's say you own sportsite.com and baseball.com. Your main site might be sportsite.com and you'd prefer to have a setup as baseball.com and sportsite.com linked in the menu than baseball.sportsite.com with the baseball.com redirecting to the subdomain. The latter option is pitiful if you have such a nice domain to use. But if you've got a small section for your company, it might be intranet.sportsite.com and another area called advertising.sportsite.com which isn't expected to get many, if any page views, except off the main site itself. That works.
My site has the same principles. I have a great main domain and several excellent "brand domains" that can run simultaneously and be linked through the header. Sure it would be ideal to put them all under one roof but sportsite.com/baseball/ as a URL is truly mediocre and undermines the value of those great domains. Now for the life of me I'd love to get multisite manager running.
[Anyone interested in lending a hand or for hire for what should take all of a few minutes, I'm all ears. I don't know complete protocol here but can be reached at slinky which is at news guy d com (you can figure it out but spiders won't, lol.)]