There is no way for users to opt for a default search option to exclude documents. Adding "-filemime:pdf -filemime:djvu" verges on being incomprehensible for most non-tech users.
This could be usefully added as a site user preference, or made another field in the Commons search UI.
This is an issue made more significant recently, with the IA books project adding a million PDFs to the collections on Commons. Consequently even simple (non-document type) searches like "cats with flowers" are returning lots of uninteresting looking PDFs in the top search returns, unless you happen to be very interested in Seed Trade Catalogs.