I've been trying to use FamiTracker on Linux for a while now, and I finally found a way that works.
1. Install Oracle VM Virtualbox
2. Make a Windows XP virtual machine
3. Get an ISO (legally or not )
4. Install Windows XP
5. Download the famitracker .exe or copy it to your virtual machine
Note: If you are having sound problems, go to the famitracker config (File > Configuration), go to the Sound tab, and change the device to something else (mine says Intel integrated audio)