I've been playing about with various methods in an effort to extract my final fantasy tactics save file from an original cart, but have not yet managed to extract anything that works.
If it's any help to the OP:
Method 1 - Try GBALDR, hold R2 whilst loading, this will extract the ROM and .sav file. My FFTA save didn't work though (I'm assuming this could be because it's not an SRAM save).
Method 2 - EEPINATOR, seemed to work well, but as far as I can gather only takes SRAM, so didn't work for me.
Method 3 - Use cart_save (download from this site). Requires you to hot-plug between 3-in-1 type device and actual gba cart. Again, I didn't get a working save file from this.