Setzer, the flickering on Harvest Moon (and pretty much everything) on emulator will look weird because of the refresh rate. On systems like the GBA or on arcade monitors or TV sets you have a stable refresh rate. Same goes for most or all CRT monitors, but not sure there. But on LCD screens this does not usually happen, so you get tear.
Anyway, for those who wanna play GB stuff on emu use KiGB and turn on "Mix Frame" under Option > Video and you will get a nice ghosting effect which looks very very close to the real thing.