I don't know about actually making me cry, but these moments in ST III do stir my emotions:
- Kirk's reaction when he's told that his son has just been murdered.
- Kruge getting kicked off the cliff and being swallowed by the lava. Good bloody riddance!!
- Kirk and Spock being beamed up as the Genesis Planet tears itself apart around them.
- The last scene, with Spock taking his hood off and looking at Kirk, and then the original TOS theme tune as the sun comes up over the Vulcan horizon, and then it goes into Horner's theme. Beautiful and epic.