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It is obvious that these sites are not "separate" in the sense that they contain information from different entities. So they must be separate in one of the following senses:
1) They are on the same subject, but they don't link to each other. In other words, the webmaster of each one recognizes that the other site -- even though he has a personal interest in it -- is so worthless to users that he doesn't even bother to link to it. And we say--if not you, why us? It's spam.
2) They are not exactly on the same subject, but they are on "fraternal" subjects. That is, a business retailing forks, knives, spoons, and coffeecups creating a separate "site" for each product line. This is also spam. Basically, one retail establishment, or one "directory" proprietor, one listing.
3) They are on such different subjects that they have no relation at all: geocities/johndoe, created by the Lilliputan druidic nose-flute performer, and geocities/richardroe, created by the egotistical gerbil-hunting bridge player. It doesn't matter whether they are on the same domain, or subdomain. They can be considered for separate listings.
4) Diverse company (or prolific webmaster with diverse interests) chooses to keep all of its divisions at one site, each given their own subdomain (classically), subdirectory, or portal (database-driven, human unfriendly URLs). With modern web hosting, there is no longer any real difference, as hutcheson says. I'll call them all "subdomains" for purposes of discussion.
Each subdomain is indeed eligible for review and possible listing. Examples: FairIsaac, DTThomas (UK domain), and the Insurance&Finance Research Station (webmaster with waaaay too much free time). Similarly, a diverse company may choose to actually have different, individually listable, domains. Example: Ford.
The bottom line is that unique and useful content is king. Neither narrow-content subdomains nor fat subdomains, flooded with chaff available elsewhere, qualify. Nor do five hollow domains of an over-eager eBusiness. Build and maintain one good site. If you end up growing and diversifying, your site(s) can reflect it, and diverse content can be submitted to appropriate ODP categories.
-- Rich
...Each subdomain is indeed eligible for review and possible listing.