The USGS has announced that the National Atlas will be taken out of service as of September 30, 2014. According to the detailed product availability information, much of the data will be available via the to-be-enhanced National Map system, or as data downloads "at no cost from Earth Explorer".
This transition appears to be mostly a resource realignment (basically reducing the number of sources and web sites they need to maintain.
In addition, the USGS has also announced that "[L]ater this year we will deliver these new framework datasets at one million-scale: networked hydrography, updated streams and waterbodies, streamflow gaging stations, cities and towns, Federal lands, Indian lands, wilderness areas, and urban areas."
For those of you who are using USGS WFS and WMS services, based on the National Atlas, be warned that the services will be taken away September 30, 2014, but that the USGS is " currently evaluating options for continuing small-scale Web services beyond September 30, 2014, and will provide updates here."