I posted these in the "Top 10 Moments..." thread, but some fit here as well.
The destruction of the Enterprise in ST III. (I said "My God" at the exact same moment as Kirk there. My wife whispered, "How did you know he was going to say that?" "I didn't." I told her with tears in my eyes. I actually didn't think they would do it).
Kirk being made Captain again at the end of ST IV. (I was cheering along with the crowd). It was tears of joy here.
Kirk falling upon hearing of David's death in ST III. (Another tear jerking moment for me, and I did not even like David, but I really felt Kirk's pain there).
Kirk's "I lost a brother once..." conversation with Spock at the end of ST V. (Very nicely done scene).