I just watched The Doctor's Wife for about the 20th time last night lol.
I cry HARD at the end of School Reunion. Even though Sarah does get to see the Doctor again, four times actually, the whole "goodbye" thing kills me, especially with Elisabeth Sladen having died last year (I didn't realize she was dead until about 10 months after she dies, and I cried when I found out). If I REALLY want to cry, I'll just watch a Sarah Jane tribute. If that doesn't do it, nothing will. I'm sure I'll cry like a baby when Sarah Jane leaves the 4th Doctor, and I know it's coming up - I think I only have 3 or 4 serials left. My favorite companion leaving my favorite Doctor
I get a little misty-eyed for Girl in the Fireplace, Doomsday, The Doctor's Wife, God Complex and Voyage of the Damned. I cried at the end of Planet of the Spiders (3rd Doctor regenerates). I cried for Father's Day, Last of the Time Lords, End of Time, Journey's End, Waters of Mars, and The Power of Three. I'm sure there are some I'm forgetting.
But the ones that made me cry most were actually Torchwood. The end of the second season was so sad, and then came Children of Earth. Oh god. I cried so hard at the end of Day 4 I had to take almost an hour break before watching Day 5, and then as soon as Day 5 started I was crying all over again. I cried a few times during Miracle Day, too, but not like I did for Children of Earth.
I've cried for Sarah Jane Adventures, too. Especially Goodbye, Sarah Jane, Death of the Doctor, and the end (epilogue?) of the last episode. The last season (well, half season) isn't on Amazon, which sucks. Not even available for purchase, it just...isn't there.