Definately include both teams. Either do a seperate design for each, or go with something like a double-sided box.
I'd go with like blue on the left and red on the right as a background, and both flags incorporated into their respective colors.
Im the only one who said Brenodi? We have sort of a Brenodi theme going on; the background screen is afterall is a bren soldier... But making a combiantion of both will possobly be more fun...
If you really want to make the double-sided box work, make a flap like on the HL2 box (and most others) on each side.
Anyone here remember the FarCry box? Make it like that. Have the outside of the box be neutral (use some mapping and ingame screenshots or something), but when you open the little cover on the front, one side is blue, and it abruptly transitions into red.
Seriously, though, those flower things screw me up. My desk shelves are designed for jewel cases, not giant flower plastic cartidges. I've got Black and White 2 and Dungeon Siege 2 sitting here, and they're taking up as much space abreast as 6 normal cases. So damn annoying. I like the openable flap idea. You should be able to get equal representation for both sides with that.
The thing that irks me about the cardboard ones is that nowadays you'll get the game disc in a plastic sleeve. How am I to store that? In the days of yore you'd get a plastic cd case with it. But yes, the flap on the front it a great way to allow for more propaganda.
Personally, I'm a fan of the standard plastic DVD case. If you were to use a jewel case, you could always make it reversible.
I dont know if anyone owns ut2004 legally, but I really love the box it came in, my Civ4 box is the same size. They are just the right size for everything to fit in it and not hueg like those old cardboard boxes. Dvd Cases are nice too, has more space for some awesme game art than just a jewelcase