Ryan, I have to say that you do bring a great point here and kudos to you on that. I think I may have jumped the gun a little bit in my initial response without considering the exact situation.
If you look at site like Compendium, along with Smashing Magazine and Noupe, they use this same method. Although, they a lot of high quality content, get tons of traffic and their category and tag structure are highly organized. This does work well, but from my experience, if you don't have all of those keys in place then you won't rank well for those categories in search results. On the other hand, here at SEOmoz, they do not have their tags and categories indexed, but they have the organization, traffic and content. Although, the only difference is that SEOmoz isn't using URL friendly slugs for these categories...
Maybe the better suggestion to Jared should be, try it both ways. Use noindex, follow at first for a month or so, then switch to indexing them. Test each method and see what results you get for your blog. It won't hurt your site in any way. I would just suggest that if you are going to index categories that you make sure you have thought through your level of organization.