Is SpatiaLite the only single file/db spatially enabled exchange format?

In terms of OGC Simple Feature SQL specifications, Spatialite is the only open source implementation on a single file basics. For this reason (and others!) it has major benefits compared to other flat vectorial formats like shapefile etc...

Being fully supported by GDAL as an "official" OGR driver [0], this is a warranty for future support of major GIS Desktop software (they all use the universal GDAL).

Currently only QGIS is able to read (and write) it, so if you want an exchange format directly readable/writable from your software without exports to other formats maybe it is still not your best option, if you are not using QGIS.

If you need an exchange forma though, as already suggested, you can use a whatever supported format from GDAL/OGR [0] and then import back to a spatial db.

Note that if Spatialite will implement topology, as I have heard, it will be have a major benefit compared to other plan formats (like shapefiles for example).

[0] http://www.gdal.org/ogr/drv_sqlite.html

[1] http://www.gdal.org/ogr/ogr_formats.html

It really depends of your needs. I also think geojson, gml, citygml, and the google kml could also be considered as spatially exchange formats.

Although it lacks support outside of ESRI, Personal Geodatabase would be a good choice, and has industry adoption. In terms of adoption AutoCAD formats could also be considered.