Software: hotpants, PostgreSQL, realbogus (Bloom et al. 2012) scamp (Bertin 2006), sextractor (Bertin & Arnouts 1996), sncosmo (Barbary 2014), swarp (Bertin et al. 2002), matplotlib (Hunter 2007), numpy (Van Der Walt et al. 2011).
The AASJournals now highlight software using a paragraph trailing the acknowledgements that lists all software used in the paper's analysis. The software doesn't need to be mentioned in the main text; context-free mentions can be placed here.
The format is a 2 item tuple containing the short/common name of the software, and a citation or URL for the software.
In principle this section could be data mined. At the moment it is just a free paragraph in the XML, but could be given more explicit markup to aide in data mining reuse and indexing.