I've been using ZSNES for many years, and I love it. I recently built an arcade cabinet using an old PC running Xubuntu 9.10, and decided to include this emulator. I used apt-get to install it.
The problem I'm having is with the bilinear filtering. It works just fine when I run the emulator from the Applications menu and then open a rom, but it does not (always) work when I run it from the terminal window with a rom name parameter. This also occasionally causes the program to crash entirely, and I cannot relaunch the emulator without restarting the system.
As a workaround, I have bilinear filtering turned off and I am using the 2xSaI filter instead. This allows successful operation, but does not look as nice as bilinear in my honest opinion.
Xubuntu 9.10
AthlonXP 1500
320MB RAM
nVidia GeForce fx5200
Yes, the system is quite dated

Thanks.