The last Strigon pilot you shoot down in the Moloch Desert mission to accomplish it...Genre Savvy much?
Strigon pilot: "No! He got me! Aaaaaaaaaaaaagh!"
...does it really have to be made obvious?
There's also a certain Mook in a mission somewhere in a Bind of Doom:
Stovie pilot: "I've got an ejection system malfunction! I can't eject! "
..or something along those lines.
AWACS Ghost Eye's jokingly uttered dialog with the other pilots at the end of some missions regarding Avalanche to be reported as shot down in Mission 2, or Sky Kid's 'bedtime' in Mission 6.
In Mission 12, we get this from Garuda 2:
Shamrock: "We're not a couple of private dancers for the military, you know.." Maybe a stab at the 'don't ask, don't tell' policy.
Or it could just be a complaint about how Garuda Team gets assigned insane assignments and is expected to fulfill them without question. Not everything is a political statement.
The Aigaion, and its escorts. Armed to the teeth, escorted by some of the best pilots available, and most importantly huge. Unfortunately for them, being so huge meant a sluggish A-10 could simply fly up to them and bomb them. Not even missiles, just going ahead and dropping a big, fat, unguided bomb or three on them. One can't help but find that little design oversight humorous.