Since I already own my number one cab (Robotron), my current top 3 are:
1. Jaleco Pony Mark II - though not a dedicated cabinet, the size of this jamma cabinet is wonderful. I love the smaller comfortable sit-down style, the angle of the screen, and sleek boxy lines. Set the screen to vertical, and you have the perfect shmup cab!

2. Baby Pacman - (a fully working one) Some people give this game flack for being half-way between both worlds. Yeah the video game part isn't exactly the same as traditional pacman in terms of ghost behaviors and speed, and yes the pinball play isn't too deep, but I really think the meshing of the gameplay between pin and vid is great. Having to earn your power-pellets with the drop targets, the risk/reward for hitting the blue drop target for big points/extra life, the video game upgrades to the tunnel play and fruit spawning and the progression of levels though the video game itself. This game is so much fun for those who like both vids and pins, with the convenience of being in one cabinet. And there's no way to emulate this game in Mame!

3. Gyruss - Great game, great music (in stereo!), loud/flashy looking cabinet
Definitely in my top favourite games of all time. I already own the board (with jamma adapter, so I lose out on the stereo sound) but it's not the same as having the original cabinet with monroe sticks. I get by playing on JLW's with an octo-gate, which is actually pretty good.

Honorable mention: Lunar Lander - playing this game on the thruster controls and lit-up front panel, in glorious vectors had me completely smitten over this cabinet.