In no particular order:
Stage 17, Tour 06: Say what you want, but that was the most epic stage win on this side of the millennium. Landis pouring water on himself like mad, running Sinkewitz into the ground, the field behind disintegrating on the final climb. Can still remember the feeling of watching a significant piece of history while it was happening.
Fedaia, Giro 08: The most beautiful climb on earth. Again, say what you want. It's always fascinating to watch Sella gain time over the pack on the last climb, and I love brave escapes in the mountains. The action among the favourites behind is also really good.
Finestre/Sestrieres, Giro 05: I'm hoping Rujano will gain the necessary time everytime I watch it. It has the coolest climb on earth in Finestre, a breakaway attempt by the GC guys, Savoldelli's beautiful descent, and the drama on the last climb. There's also something about winning a mountain stage in the climber's jersey (goes for Fedaia as well).
In my list of heavy rotation stages, there are also various Basso exploits from the 06 Giro, the entire 07 Tour, some of the dramatic stages from 07 Giro (love those Saunier Duval 1-2s), the Sastre stage in 08 Tour, Angliru 08 is very fascinating, Valverde's Ventoux ride in the Dauphiné, and of course some of the great Tour stages with Armstrong, Ullrich and/or Vinokourov. I especially like the one after the 03 mid-race time trial, where Ullrich attacked with some serious determination, even though it didn't really work out.
There, that should just about cover my main favourites
