Generally, Sub-directories are better. Though I use subdomains all the time (ie: wiki.site.com, forum.site.com), more for practicality reasons or very specific circumstances (ie: custom rendering of site in a sub-domain that replaces the logo etc).
That said, different site structures may require different architectures so you might want to do different types of backlinking if the structure or logic is different. That way subdomains would be preferable however you might as well get a new domain for that like Zapdos suggests (unless costs are a factor, ie: 1000s of subdomains).