[Note: This flag is from Cruzeiro do Sul, Acre, Brazil. For me, the simplest demonstration of Crux majesty]
Firstly, it's important what the Southern Cross means: the South, its ancestors and its lands. During the Antiquity, it was visible in southern Europe and other similar locations. But, in the transition to Middle Ages, approximately, the change of Earth axial inclination hided it until, at least, some thousands of years.
The first time the Southern Cross was saw again by an European was in 1500, during the Discovery of Brazil, by Portuguese astronomer João Faras. Since then, navigators adopted the Crux in the same way the land natives was using it since immemorial times: as a reference mark to Southern Pole (my post about Antarctic flags shows one flag refering to this fact). And it's as a symbol of geographic position that the Southern Cross is used in flags, etc. See a small gallery with some of these flags:
[Click on image to zoom]
The Southern Cross is frequently seen in flags of Argentina, Australia, Brazil, Chile, New Zealand, Papua New Guinea, and Samoa, and it's featured in many of Australia and New Zealand proposals to new flags.
I'm a great fan of Southern Cross, but I must to tell a bad note: the Southern Cross is tattooed, in Australia, with a connotation of nationalism that sometimes comes near xenophobia. However, I think until many Australia recognizes the Southern Cross as the incredible symbol it is.
If you want to give your opinion about the post or the Southern Cross use in flags, feel free to comment. Thank you!