I guess it's supposed to connote triumphalism. As in "yay, it finally shipped!" The NetBSD logo, itself based on a cartoon of daemons hoisting a flag like at Iwo Jima, has many of the same connotations.

Back in Windows 3.1, by going to ProgMan's About box and Ctrl-Shift-Clicking the Windows logo X amount of times, you could trigger an "easter egg", one screen of which was a flag waving with the Windows logo on it. Another of which was a credits scroll with a cartoon figure that had one of four faces: Gates, Ballmer, the Windows dev lead at the time (I forget who but he had a beard); and a creepy looking teddy bear (some sort of internal mascot for the Windows division).

Good times.