Autopano-SIFT by Sebastian Nowozin automatically creates control points for groups of overlapping photographs, it can be controlled from within the Hugin GUI front-end. See archiv.org version of the autopano sift page for details.
Functionally, autopano-sift is very similar to autopano and the two can be used interchangeably to a certain extent.
There are both command-line and GUI versions of autopano-sift. There is a tutorial for Using Autopano-SIFT With PTGui.
Autopano-sift is Open Source and written using C# and mono. The use of the Scale-invariant feature transform algorithm is restricted by US Patent 6,711,293 awarded March 23, 2004 to the University of British Columbia.