The solution to get them back was as simple as it was surprising.

Running desktop-file-validate on the *.desktop files in ~/.local/share/applications produced a deprecation warning:

daniel@seppel5:~/.local/share/applications$ cat zotero.desktop
[Desktop Entry]
Encoding=UTF-8
Version=1.0
Type=Application
Name=Zotero
Icon=/home/daniel/.zotero/zotero_128x128x32.png
Exec=/opt/zotero/run-zotero.sh

X-Desktop-File-Install-Version=0.22
daniel@seppel5:~/.local/share/applications$ desktop-file-validate zotero.desktop 
zotero.desktop: warning: key "Encoding" in group "Desktop Entry" is deprecated

Simply removing the offending line that started with Encoding: did the trick, all my programs reappeared in the Unity dash.

find ~/.local/share/applications -iname '*.desktop' | xargs sed -i '/^Encodi/ d'

It’s probably a good idea to make a backup first.

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