I've read that the legacy version works under wine, I haven't tried that yet.
I've tried the latest ng version in wine, which installs and runs, but fails to detect the serial ports. Since the ng version is a java program, I've tried running it through my native java version, but that didn't work out either (it kept looking for classes with "win32" in their name). Perhaps either of these approaches could be made to work, but not out-of-the box at least.
To flash firmware, at least to S2 (ZB) devices, there is the xbee-comm
tool (haven't tried that yet either).
To configure a module running in AT mode, you can of course use a serial console program like minicom or screen.