I was kinda bored, and thus decided to try to do this. I couldn't find an easy way to do it with SEDE, so I hacked together a thing in Python. It's on GitHub.
Here are the results (this can, and probably will, be made better):
6 x http://notepad-plus-plus.org/
6 x http://www.gimp.org/
5 x http://handbrake.fr/
5 x http://www.autohotkey.com/
5 x http://www.ffmpeg.org/
5 x http://www.irfanview.com/
5 x http://www.jetbrains.com/idea/
5 x http://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/
5 x http://www.sublimetext.com/
5 x http://www.virtualdub.org/
4 x http://avidemux.sourceforge.net/
4 x http://brackets.io/
4 x http://en.wikipedia.org/wiki/Emacs
4 x http://getgreenshot.org/
4 x http://gitlab.org/
4 x http://jdownloader.org/
4 x http://www.chiark.greenend.org.uk/~sgtatham/putty/
4 x http://www.code42.com/crashplan/
4 x https://filezilla-project.org/
4 x https://www.gnu.org/software/octave/
Note that I'm only showing links that have more than three occurrences. Anyone that wants to contribute can fork the repo and make a pull request!
Edit: I added duplicate detection, now the same link in an answer more than once only counts once. You can see the old, non-dupe-detecting, results in the revision history.