I use FPSE on a regular basis. It doesn't work as flawlessly as it does on Tegra devices, but it's certainly solid.
If you have it installed, try the following steps.
1. Go to manage apps, and clear data.
3. Re-install from the market
4. Upon opening, the app will ask you for a bios. You should already have the bios downloaded. If not, I have attached it. Remember to drop the .7z from the file extension. XDA won't let me upload it without this.
5. Before opening any games, hit back a couple of times until you get to a white screen, then hit it again to bring up the menu.
6. Switch to OpenGL before you do anything else. You lose some compatibility, but the difference with 3D games is staggering. Do this by going into CONFIG>MISC>SWITCH TO OPEN GL>DOWNLOAD FROM INTERNET. The app will need to restart. You can skip this step if you want, but your graphics will be dramatically better.
7. Open the app again. Once again press back until you have navigated to the menu. Do this before doing anything else. Change the following settings:
Check Fastboot on. This will skip the playstation boot up screen. The other settings in that option do nothing for the GS3 that I can tell.
Check spusync, and enhance sound emulation. This will improve the sound, but if your game stutters or won't load, then you may want to choose null sound plugin. No sound, but better compatibility.
I only leave 2 things checked here. Frameskip checked, with framelimiter UN-checked. Then check special framelimiter farther down. Leave everything else un-checked.
9. Configure the gamepad using gamepad. This will be personal preference, so no tutorial here.
10. Go to MISC>Save config as default
You should be good to go. Remember that it's important to not have corrupted ISO's. Also, video settings will stay the same across all games. Sound settings, and gamepad settings that are changed once a game is loaded, will be specific to that game.
If you can't get your game to load, try another one. If you can't get any to load, then you may be having a different issue. Hope that helps.