Lots of good ones! Here's some of mine that springs to mind:
1. The death of Kai Opaka. The emotion Nana Visitor conveys, the anguish on that prison moon. It was the episode that made me believe DS9 could be great.
2. At the end of the Voyager episode "Year in Hell," Janeway reaches out to embrace Tuvok saying good-bye. For just a *moment* Tuvok breaks and embraces her back. That moment between them...get me every time!
3. Relics - a love letter to James Doohan.
4. The Picard scenes in the TNG episode "Family." You see the human pain behind the assimilation. A great Patrick Stewart episode.