Though I'm not sure what my favourite mission is, one that I do really like is Exodus (SM3-05), the first mission where the player is leading the blue lions. It's more or less a simple escort mission, but the opening scene of a Sobek and a Moloch destroying one another, along with the Vasudan's speech gives the perfect atmosphere of a system and an alliance on its heels from a massive Shivan invasion. As a Fredder I weigh heavily on the importance of the opening few seconds of a mission, its the only scene that the player is guarenteed to see, so make it a good one. Bearbaiting is another favourite for exactly the same reason. Whereas something like Clash of the Titans II would fail somewhat, because the convoy is supposed to have been under attack but you don't arrive during one, instead you arrive just after and watch a few allied fighters blow up for no particular reason.
