With Snow Leopard, Apple changed the "International" preference pane organization, and also altered the input menu icon so that depending on the options in the menu, it removes the country flag. This is a subtle change, but I personally liked having my country's flag in the upper-right corner of my computer.
The non-flag menu icon displays when only the "Keyboard & Character Viewer" option is selected to be shown in the menu, which may be the case for many people who use one language but also use the keyboard viewer to access hidden symbols. If you enable more than one input method (keyboard layout) and then select the desired one, you can regain the flag of your choice in the menu bar.To do this, go to the "Language & Text" system preferences and go to the "Input Sources" tab. Then check any of the input methods in the list and the input menu icon will change to a flag.
Optionally, if you do not use the keyboard and character viewers you can uncheck them in the "Input Sources" list and just have a single keyboard layout selected. Then be sure the option to "show input menu in menu bar" is checked and the flag will appear.