My Today Extensions in El Capitan are all missing
Figured it out. 

There's some solutions for Yosemite I found online but none of them worked for me. 

Turns out part of the issue is that El Capitan introduces System Integrity Protection (SIP) which is causing the bug, or it's preventing the fixes from working, or something. 

Anyway I got the answer from here. Basically you just


Reboot in Recovery mode (CMD+R at the chime)
From the recovery menu pick Terminal
Run this command to (temporarily) disable SIP: csrutil disable
Reboot into El Capitan
Verify that the extensions are back in the sidebar and in system preferences
Reboot in Recovery mode again
At the Terminal re-enable SIP with run csrutil enable
Reboot back into El Capitan. Everything should still be back and all is well.