This was after I went in to change the "Default notification", and nothing was checked so I chose "CyanPing".
Checked in WhatsApp > Settings > Notifications > Notification tone, and same thing too
Nothing shown in Apollo. I had a couple of mp3s in /sdcard
Then I checked Google Play Store for any apps to be updated. Although I can't be 100% sure, but I'm pretty sure that ROM Manager's update 5.0.1.2 was the cause (updated earlier in the day). The description for 5.0.1.4 seemed to make sense to me.
5.0.1.4 Fix bug that places .nomedia file in the wrong directory if directories are missing.
5.0.1.2 Add Restore ROM Manager feature.
Updated ROM Manager but problem still persists. Rebooted and everything was back to normal again.