By far my favorite was the one where you fly with the Valkyries and the classic song "Flight of the Valkyries" is playing. Whoever thought of that mission was a literary genius and deserves praise!
Hmm, mine would be the "Sabre mission of Awesome" a.k.a. Nephele 4 (not to be confused with the "Sabre mission of Doom" a.k.a. Vega 1), in which you get to fly the Sabre.