The mac command line tool works flawlessly on 10.8, I'm using it with no problems at all.
Here's a short step by step noob compatible set of instructions
Download the binaries and extract them.
Open Terminal from Applications/Utilities.
In Terminal type "cd" followed by a space, then drag and drop the directory containing the tool you just extracted onto the Terminal window, that will insert the path automatically. Press return. (The command should look something like "cd /Users/yourusername/Downloads/ems-flasher-0.03_macos_10.6/"). That will tell your command line to change the working directory to the one that contains the tool and what it needs to work.
To backup your sav, type "./ems-flasher --read filename.sav" replacing filename with what ever you want (but keep the .sav extension, it tells the tool you want to back up the save data and not the rom)
To flash a new rom onto the cartridge type "./ems-flasher --write --bank 1 somerom.gb" ... change the number behind the --bank to 2 if you want to write to bank 2 (the one you get after powercycling the game boy). You can use drag and drop here too, to automatically insert the path to the rom you want to flash, or just copy the rom to the tool's directory and type its name.
You can autocomplete file names in the terminal by pressing tab. You can recall previous commands by pressing up so you can re-use them or edit them.Hope that helped.
So helpful for real. Thank you. Will try this out posthaste!