Well, at this point, I don't think it really matters if I post these, especially since it's not likely that anyone will want to abuse the passwords just to read ahead
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Prelude - NO PASSWORD
Mission 1 - HOSTILE
Mission 2 - CHISEL / HAMMER
Mission 3 - ARRIVAL / INVASION
Mission 4 - LAUNCH / SCRAMBLE
Mission 5 - WORKSITE / EVACUATION
Mission 6 - BUGS / PLAGUE
Mission 7 - CAUTION / HASTE
Mission 8 - ROCKS / STEEL
Mission 9 - INVOCATION / INCANTATION
Mission 10 - LIBERATION / GOODBYE
Where there are two passwords, the first is the one you get if a) you have the Fralthi and b) you haven't lost Beaufort. The second one is what you get if you lose the Fralthi OR (in the case of missions 4 and 5) lose Beaufort.