If you count pinball machines -- they were in arcades, too -- then it would be "PinBot," hands down. Otherwise, "Last Resort" on the NeoGeo.
Second would be "BallBlazer" on just about any platform: Atari 5200, Commodore 64, Atari 8-bit. Honorable mentions would be "CyberSled," "Xevious," both arcades, though several home conversions of "Xevious" are quite nice (including the J2ME recently released.)
