Miramanee's death scene (yes, the music really makes it happen)
Leila coming out from under the effect of the spores,
Charlie wanting to stay, stay, stay....
And also, in "Metamorphosis" when Nancy/The Companion is looking through Nancy's scarf. The symbolism was perfect: she had irreversibly changed.
At those four moments, I've shed the fucking tear, man.
The end of "All Our Yesterdays" always gives me a lump in my throat.
Since we're discussing TNG episodes too, I've shed the tear was the end of "The Offspring". Not at Lal's death, though I was welling up, but when Data announced that he'd integrated her program, it just came gushing out.
I've also shed the tear at the end of "Darmok", when Picard speaks the Tamarian language to Dathon's executive officer. That was a brilliant moment.