n0tttt

I assume you want to go for pre-re. I think both emulators have some issues with pre re so I don't see much of a difference here (but I'm honestly no pre renewal player and don't know the exact differences) . Else content wise for renewal rA is ahead.
As stated here, Herc works a lot more efficient and is cleaner. But it's biggest advantage is of course the plugin feature which basically works like an import folder for source code.
The mana world is running Hercules with a plugin on steroids, so you can see with plugins you basically can build a whole new game around the emulator.
https://www.themanaworld.org

My partners and I decided to go with Hercules after all, since we're running pre-renewal. Thanks for the input.
 
This seems like a very common question for people though, might be good idea to keep a permanent topic listing the differences.

Personal tip: eAmod is buggy and that one is not updated from long time. I suggest you to use some other emulator