Hmm weird thing, I tried Legend of Zelda: Phantom Hourglass on different emus and the only one that played it was ideas, both neonds and desmume acted the same giving a black screen with 1fps at the top but on ideas it played fine if the sound plugin was turned off however I couldn't play it any further than some point because it required microphone input which no emu has right now.
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Motherboard: Asus RAMPAGE Formula
Processor: Intel C2D E8400@3.01ghz
Memory: Corsair XMS2 DHX 2gb DDR2@800mhz PC2-6400
Graphics: Asus Geforce 8600GT 256mb
Gamepad: Saitek Cyborg Rumble Pad