I downloaded a shapefile of USGS DOQQ boundaries a few years ago and cannot seem to find one now. The attached image shows an example of the shapefile I'm looking for (green polygons showing the quarter quad boundaries). Where can I download a shapefile covering the contiguous USA that shows USGS DOQQ boundaries with relevant attributes?
The USDA Data Gateway has layers available for 1:12k quad footprints. Not sure if you can fetch the whole U.S. or not, but you can get them by state. Also, you can drag a custom AOI onto the map and get some pretty big chunks it looks like.
You can get the indices from The National Map in pretty big pieces, it won't let you download the whole country at once but it wouldn't be too terrible to download 4-5 large pieces and then stitch them back together. Well, it shouldn't be...
The index that I have is from ESRI, from the metadata it looks like it shipped with the map data package they used to sell as an add on to ArcGIS (perhaps they still do). I've also seen some state agencies distributing nation-wide quad indices - try your local(ish) BLM or Fish and Wildlife website, they are often good stores of spatial data.