Unless you want to be running though an area with few/any forced fights for an hour or more, don't bother trying to find wonder rocks. Just go through all the bonus dungeons and you might find one.
If you do want to take the time to farm (if that's even the right term) for one, then I'd suggest running through the first half of the Millennium Forest (Lost Sanctum) in the Middle Ages then back to the village. Just remember that finding one like this will likely take at least an hour or so. --- For the "End of the World" spell, press Control, Alt, Delete.
I don't know if it means anything, but after climbing Mount Emerald like 15 times or so, I finally decided to kill all the enemies on the screen then come back and BAM... there was one sitting right where everyone usually says it is - one level below a forced Hercules Beetle (?) fight...
--- "Thou art such a pain in the...! Confound it all! I'm starting to talk like you!" - Sabin "Wow... me fail English? That's unpossible!"
I found Wonder Rocks very easy to come by in the winter portion of the Antiquity Dimensional Vortex.
As you come up the cliffside you'll be forced to battle four Bone Soldiers, and a few steps afterward there's (seemingly) good odds of a Wonder Rock being there. --- http://www.youtube.com/Zarmwhirl TASes Yoshi's Island GBA levels, MegaMan Neo, and Kirby Super Star's Arena with many different abilities.
It only took me about 15-20 minutes. Here is what I did:
-Magus, Ayla, and Marle were all above level 60 -600 A.D. in the LS forest located north (the place you had to get the golden hammer) -Equip Ayla with a Haste Helm, and for the Acc., equip her with the Drill (the thing that raises the rate of charm) -Ayla's speed was set to 13 -Set your game status to Wait Mode, instead of Active Mode
The Wonder Rock always spawned in the same spot, and it is after the first mob (you can skip him) and around the turn. If he is not there, get out of the forest and go back inside the forest to reset the place. Keep trying until you encounter him. When you do engage a battle with the Rock, it may escape. If it does, repeat the process and fight him again. If you are lucky, he will attack you. This should give you enough time to quickly go to Ayla's techniques, and you are going to want to Charm it. I got it off the first try. Not sure if that will always happen. If you manage to defeat it, you get a nice amount of EXP and Gold. Hope this helps out.