I had a clear cut answer for this going in the thread, GameCube, but then I see handhelds are included.
Haven't played Virtual Boy as it wasn't released in Europe, so I won't be counting that one. Have all the other ones though. It comes down to either GameBoy Advance and GameCube really. 6th gen was disappointing altogether anyway, such a farcry from the 5th gen. In fact, the GameCube is the only Nintendo system I currently haven't hooked up to a tv and is actually put away in it's box right now. I'll vote for GBA, if only because I've played more good games on GC than on GBA.
GBA is also the Nintendo system I've got the least amount of games for (WiiU not counting), only 7. Compared to 8 already on 3DS as of yesterday. Worse, of those 7 GBA games, 5 (!) are remakes of NES and SNES games and the other two are Zelda Minish Cap and Mario Kart Super Circuit. Coincidentally, these are also my least favorite installments of those series, unless Four Swords is counted in Zelda, which is also GBA anyway. Granted, the Ambassador Program on 3DS revealed to me that I should've bought Metroid Fusion and Fire Emblem Sacred Stones at least, especially Fusion is a brilliant game.
From least favorite to favorite excluding VB and splitting GB and GBC (3DS and WiiU placement subject to change):
GBA
At least Nintendo on the rise again with the 7th and 8th gens
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