for a "main" blog that is less splog like I would make it
www.domain.com
for feeder type or more splogish type blogs I do those on subdomains.
for SEO if you have a couple decent inbound links to a subdomain it's going to get traffic. Heck I've got some that are all in sup index and they still get plenty of SE traffic. splogs I just rip and move on. see what happens with them and learn from them. I don't focus that much time on going back on them. Learn and move on.