All the dataset and layer creation options which are supported by the corresponding GDAL driver can be used as "OGR creation options" in the Save as... window. For shapefile the available options are documented in http://www.gdal.org/drv_shapefile.html. If ogr2ogr program is used directly these options are given with -dsco and -lco parameters.
In your case, add SHPT=POINT to the OGR layer creation options box. Or ARC, POLYGON or MULTIPOINT for other geometrytypes as described on the driver page.
However, if you need to do conversions in batches you may want to use the GDAL utility ogr2ogr http://gdal.org/ogr2ogr.html directly. There is a handy shortcut "-dim" since GDAL 1.10. The usage is
ogr2ogr -f "ESRI Shapefile" -dim 2 output_2D.shp input_3D.shp
BTW the OGR Creation options seem to undocumented in the QGIS 2.2 manual.