While you sleep they'll be waiting?

The story of the Wing Commander I message is a little overblown... it was indeed something that happened during development but the crash was fixed before the game shipped. (People go crazy for the story, though, so... print the legend!)

The quit messages were a fairly common thing at the time where games would have a little goodbye message before dropping you to the DOS prompt. Earlier ones were typically just thank yous but by the time of Wing Commander III they were often cute taunts on the order of "you'll be back!", which is exactly what the WC3 message means (while you're sleeping--ie, you've quit the game--the Kilrathi will be waiting for you to come back).

Wing Commander IV, on the other hand, got an in-joke from the team that I don't think anyone has actually explained...
I may just be dreaming this, but I seem to recall the DOS WC1 exit message was

'You step out of the airlock and into...'

Possibly only when you quit via the door in the barracks and not with alt+x. It's been a while since I played the original DOS version so I'd have to check.
This is the message the GOG version gives you if you quit via the airlock. (Tweaked settings to not close DOSBox upon exit)

I remember when we first got Wing Commander, my dad had to set things up so that our 80286 could use expanded memory; doing this basically required a custom boot-up procedure. As part of the batch file he built to do said boot-up and then reboot the computer for general use once we were done playing the game, he appended the message. So, when I quit Wing Commander, I was always treated to...

"You step out of the airlock and into...EMPTY SPACE! HOPE YOU KNOW HOW TO BREATHE IN A VACCUM!!

Press any key to continue . . ."