How do you query for Asset Folders? I'm building a customer portal for work, and we are storing customer-facing files on the site in an Amazon S3 bucket. I currently have it all set up as a Structure section with an Asset field. I query for each entry using its uri, and for Folder Entry Types I pull and output its children.

My hope is that I can instead query for Asset folders and files directly, and then add a few fields to Assets (through the usual methods). Querying for files is fine, but I can't see any variables to pull folders. Would I need to write a plugin for this?
Writing a plugin would be your best shot. You can use AssetsService to get all the information you need (http://buildwithcraft.com/classreference/services/AssetsService)

This might change with a future release, but the need to query Assets folders directly from a template is so rare, that I'm not entirely convinced it will make it's way into a future release at this point.