And see, the beauty of Lost is that I have quite a different take on what would make for a pivotal episode. The fact that strong emotional moments, especially relational ones, are what tie these characters together, trigger their memories, and bring them together in the afterlife mean that you could say the most important episodes for the show are the ones that establish these relationships.
So my pivotal episodes, excluding the Pilot and The End are, in no particular order:
1. Walkabout, for establishing Locke's character so beautifully.
2. Do No Harm, for being essential for the relationships Boone and Shannon, Sayid and Shannon, showing Jacks' need to fix things, and the Kate/Charlie/Claire birth scene.
3. Ji Yeon, which is my favourite Sun and Jin episode (though you could also pick ...In Translation, IMO)
4. LaFluer, for establishing Sawyer and Juliet
5. Greatest Hits, for the Charlie and Claire moments
6. The Constant, for Desmond and Penny. This episode may also be the best in really illuminating the importance of relationships and love in Lost, by introducing the idea of having a constant. One could say that everyone in The End found their own constant, triggering their memories the same way the phone call to Penny triggered Desmond back in season 4.
I couldn't limit it to five. I also am tempted to add more, as episodes focusing on Ben, Daniel, Charlotte, Hurley, and others are missing on that list.