I have always been convinced that in long-running TV series there is always a specific episode which, for one reason or another, leaves its mark in the viewer. For me one is certainly "Time of death" in E. R. With guest star Ray Liotta (unsurprisingly it won an Emmy award).
Another good examples is "One day, one room", which has its merit of breaking the usual scheme of the series. A patient with an unusual sharp mind manages to connect with House in a manner never seen before. The viewer has, for the first time, the means to see a patient being both healed by and a healer for her own doctor