http://wwws.org will consider but like any other it needs to quality. But yes, wwws.org is a little liberal.
At www.freewebdirectory.us we also accept subdomains if quality ones. In fact... www is a subdomain too
Free website Directory does for forums and directories. Basically quality sub-domains for content that should be on a sub-domain. A online store that has a different sub-domains for every product/etc would be inappropriate.
Crafty Tips Arts & Crafts Directory does, but the site MUST be on topic and comply with all other guidelines.
Word-TagCloud Keyword Directory - accepting any deep link. (sub-domain, sub-page, free blog, geocities, anything as long as the site got quality content). It's paid dir though. I hope its ok.
All the paid directories i own that are in my sig do, infact we accept any URL as long as the site follows my guidlines on the submission page... Heres the links for ease: http://www.apexurls.com http://www.seofriendlydirectory.com http://www.linksearchers.com http://www.alphasubmit.com