By flickering, I meant the flicker-transparency effect, I think its the first stage after you beat the 4 base castles. The entire background flashes in/out, which on a slow screen would look better. This sounds like a great excuse to replay this game, maybe I'll make the time later. I'm curious how it would look with some of the filter options enabled and tweaked with mednafen.
The harvest moon GBA flicker is pretty annoying, at least on emulator: its a 50% dither pattern that alternates, it can look pretty smooth most of the time, but there are times when it'll lag and be like "hey vision, you're totally fucked

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The subtle feeling of helm's flickering image earlier in this thread gives off a creepy feeling, and I think it works well for that, but I'd shy away from it in most cases.