Even if you have a single blog, you probably have multiple feeds. One for posts, one for comments, and maybe even one for each individual post's comments. Add on that the different flavors of syndication, RSS and Atom, and it can be confusing.
Posts Feed
This feed will be used by many of your visitors, and generally speaking will be used by people who subscribe to your site. Sites with feed urls in the header for auto-discovery should have this feed as the primary one, because that's what most visitors expect to get.
Comments Feed
A comments feed is also useful, but often underused. This feed is simply syndication of the most recent comments on the blog. Allowing your visitors to know that there are comments being made on a blog is one way to turn up the community feeling a notch. When visitors have a sense that there are comments being made, odds are they will be more likely to make a comment themselves, due to the perceived lower barrier to entry.
Individual Posts / Comments Feed
Taking this one step further, some sites will offer a feed for the comments on a specific post. This isn't useful all that often, since it requires a high volume of comments to make it practical to allow visitors to separate comments with this feed versus a general comments feed.
Instead, it is often more useful to allow commenters to get email updates when new comments are made. Since the life of a post eventually tapers out, this is better than devoting a slot in a RSS reader for a feed that will eventually become a dinosaur.
Multiple Blogs, Multiple Feeds
If your institution has multiple blogs, consider a way for visitors to subscribe to both with one feed. If every slot in a visitors RSS reader is valuable, offering them more content with one feed will be valuable to them as well.
We offer individual feeds for all of our blogs at the Walker, but we also have a combined feed that is offered on our main blog page. Each unique blog has auto-discovery for that blog's in the header, but also features an auto-discovery link for the combined feed. Using a combined feed allows for more cross-pollination and more readers.