1. When Homer quit his job for Maggie.
2. When Mr Bergstrom left Springfield, and Lisa, behind.
3. When Maggie was tempted by the Flanders family but still picked the Simpsons.
4. When Lisa thought she was losing her intelligence.
5. When Mr Burns was reunited with Bobo.
6. When Nelson got attached to Marge.
7. When Bart sold his soul to Milhouse.
8. When Marge reassured Homer of her love for him.
9. When Bart got caught shoplifting.
10. When Lisa dumped Ralph on TV.
11. When Apu stopped owning the Kwik-E-Mart.
12. When Marge realised she'd changed for the worse.
13. When Homer got a glimpse into Lisa's world.
14. When we found out Principal Skinner isn't actually Principal Skinner.
15. When Bart got an F.
16. When Homer's mother came back and then left again.
The original Skinner is not canonically dead. He is simply another person. An earlier version of this post misidentified this.