The SharePoint developers in my group seem to be going toward creating single document libraries for sites (and putting hundreds of documents of all types, Word, Excel, PDF in each) - and then "virtually" segregating and displaying the documents using custom views and filters - rather than creating individual document library folders for various document types (processes, procedures, policies, for example).
Is there any insight you can provide with respect to response time or any other user-facing impact (or on the system itself) by doing it this way (doc files in a single library) - in favor of using the "folder" scenario?