Easily the S2000. Snap, snap, snap and away you go. Nice and short throw. The R32 GTR was pretty alright too but throw is not as nice as the S2000. MX5 was also pretty good (6 speed box).
My old 94 WRX was too notchy, didn't like it much. But the worst has to be the new VW Golf DSG sequential box. Takes about a second/second and a half to change gears once you hit the paddle.