1) The Becoming (the first epi I ever saw, and still my all-time favorite--Cristina's speech about Burke was one of the most moving scenes in the series, and the gay soldiers' couple were amazing)
2) Time Warp--Bailey and her Nazi were hilarious, and the GRID/AIDS patient's case was so poignant. It made me understand Ellis and the Chief's relationship much better, too.
3) Into You Like a Train (that scene where Mer cries out, "what about her?" when they give up on Bonnie is heartbreaking)
4) Grandma Got Run Over by a Reindeer (I, too, am a huge fan of that scene at the end where Mer, Izzie, George and Doc are all lying under the Christmas tree. It really speaks to how incredible this show was in season 2, and how close their bond as roommates was. Even though I've loved the seasons after, there's something so heartwarming about season 2 that I miss very much).
5) What a Difference A Day Makes (I cried my heart out at Izzie's wedding)
6) Stairway to Heaven (Ellen Pompeo should have won an Emmy on the basis of that scene after the serial killer's execution)
7) Time Has Come Today (esp. the scene where Derek comes into the kitchen and tells Mer he's in love with her)
8) Six Days, parts 1 & 2--I just adore the O'Malley family, and the scenes between George and Harold, esp. looking back now that both are gone, are just so heart-wrenching. There was a sincerity and integrity about George that I dearly loved and miss so much