Thought I'd report back with my progress on this:
The optocoupler works great! Since then, I've nearly finished this project. I've now got my Arduino listening for serial input from my Ubuntu box. When it receives the "open" command, it opens the garage door, and replies with "Garage Door Open!". I was initially worried about the usb/serial communication, but that was no problem.
I ended up configuring /dev/ttyUSB0 for the Arduino, then just echoing the command to that tty.. In another window, I just tail the tty to get the serial response. In front of that, I set up a simple php script to run my root command (which echo's the "o") via a secure web form.
It probably sounds chaotic, but it's really quite smooth. Works great!
Thanks again for your help guys.
-eXup