Applications Don't Show Up in Spotlight
Loading the metadata plist worked for me:

Turn off spotlight:

sudo mdutil -a -i off


Unload it:

sudo launchctl unload -w /System/Library/LaunchDaemons/com.apple.metadata.mds.plist


Load It:

sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.metadata.mds.plist


Turn on spotlight again:

sudo mdutil -a -i on


Now everything is being reindexed as expected.

In newer versions of macOS, just turning indexing off then back on again resolves the issue.