Glad you posted this because i'm in the same boat, looking to build a bartop. I have already built my own mame cab several year ago and this winter it got hit with a power surge and the power supply and hd were fried. So in the process of rebuilding my cab i was inspired to build a mini arcade.
I was unimpressed by the plans i saw out there until i saw this (images attached) i like the design a lot. Although these are not plans, the pictures are enough for me to work with. As far as the system, I just spent upwards of $600 for a new quad core 3.8ghz for my broken cab, and i don't want to spend anywhere near that on the mini. Luckily i have a friend who bought a brand new HP laptop and 6 months later the screen went bad, so she bought an all in one and gave me the laptop. it still works fine, all i need is a flat screen. If you can find a fairly new laptop on ebay with a broken screen, thats one way you can go
The controls im looking at are the ultimarc mini-pac because of its small footprint and its support for both trackball and spinner. Joystick i want something looser than the ones i got from ultimarc because i imagine it would make it hard for a lightweight tabletop cab to stay still. Trackball and spinner from ultimarc.
Some other details like whether to go with a speaker system with subwoofer or just get a flat panel with built in speakers and a few minor details to work out.
Hope these suggestions help.
[ATTACHED IMAGE - CLICK FOR FULL SIZE]