I really liked Stage 7, TdF 2007 - watching Linus suffer like that to beat the peleton by a mile.
I also liked Stage 3, ToC 2008 - the camaraderie of Gesink and Leipheimer working against the peleton.

Ultimately, I like any stage where the break wins. Kind of has that "few-stronger/smarter-than-many" aspect to it.

I never saw it live - but the 89 TdF was very dramatic. Amazing story.