Did you bother to search before asking your question..?
Your only options aside from what you've mentioned is open_agb_firm or Virtual Console injects. These are both identical in functionality and differ only in regards to their interface. They're not really emulation as they run code natively on the 3DS hardware – which means you can't use savestates or any fancy fast-forward features that you would expect in emulators nowadays.
open_agb_firm is somewhat preferable, but does not provide convenient Home menu icons, if that's what you want.
I'm not sure why TWiLight Menu (or more precisely GBARunner2) should screw up the visuals. It might depend on the particular game you are trying to run.