Here is what I have, what worked well, and what didn't work so well
Cabinet: Mortal Kombat II. Very happy with this. Roomy cabinet, nice control panel, 25" display. Acquired for $375 at auction. Eventually, I turned it into a MAME machine. The conversion is completely reversible (I didn't cut holes or damage anything). It's fun when folks come over and see MKII running on this MKII cabinet, then I hit a couple of buttons and reveal that it is a multi-game machine, then hit a couple more buttons, grab a wireless keyboard, and reveal that it is a fully functional computer, with a broadband Internet connection!
JAMMA PCBs: For a while, when I first got my cabinet, I bought various JAMMA boards on ebay so I could play a bunch of different games in my cabinet just by changing PCBs. After a while, the board swapping was just too much of a hassle.
Mobo: AMD Duron 1800. Works very well with most MAME, SNES, and Genesis games I have tried. In terms of speed, my arbitrary goal was have no discernible difference between my original Jamma MKII and MAME MKII. It achieves this.
Memory: 512 MB. No problems at all.
Video: Trident Blade T64 (driving the 25 inch arcade monitor). It's great, but... my only complaint is that the screen is scrambled until my Blade driver loads. I chose the Trident card because the ArcadeVGA card was more expensive, and folks said the Trident card had more vibrant colors. However, if I ever build another cab, I might take another look at the ArcadeVGA.
Interface: JPAC (PS2 based). This thing is awesome. Basically the heart of the system. I like the way it protects my 15KHz monitor if my video card tries to send the wrong frequency (which happens a little too often). Highly recommended.
Audio: PCI based SB Live. Was a hassle getting it to work reliably in DOS. Never did get it to work reliably with ADVMAME running multiple emulators under DOS. Works well with Mamewah in Windows though, and eventually I learned that Mamewah and Windows was the best combination for my cab. I'm not sure there is a better alternative sound card. Some folks say ISA sound cards are better, but I don't think you can get a modern, fast motherboard with ISA slots any more.
Frontend: Mamewah. I ran ADVMenu for a while, but I had various issues with it when switching between emulators or entering/exiting emulators. I think it was mostly due to compatibility problems with my 15KHz video driver, SB Live driver under DOS, etc. Mamewah is great, but my biggest complaint with it is the performance issue when dealing with large lists.
OS: Windows 98se. I started out with DOS (WIN98se DOS) but eventually discovered (to my surprise) that games ran a little faster under Windows, and that Mamewah under Windows worked better for me than ADVMenu under DOS. Windows also makes it possible to add USB game controllers and has built-in networking (which comes in handy sometimes). If I had to do it all over again, I would probably try Windows XP.
Emulators: For MAME, ADVMame (great if you like to tweak and want to get your arcade games to look great on an arcade monitor). For SNES, ZSNESW (hacked so that Esc exits the emulator) and, for Genesis, WGENS (also hacked so that Esc exits the emulator).
Joysticks: HAPP Competition joysticks. I didn't realize how sloppy the joysticks in my cab were until I replaced them with the Happ Competition sticks. They are great.
Gamepads: Cordless Logitech Rumblepad II's. This worked out nice. For games that work better with a gamepad instead of the cabinet control panel, there are two cordless rumblepads stored behind the coin door. They work great and you can use two simultaneously. Two complaints: 1) You can only activate a profile for one rumblepad at any given time; so, for example, if I want to assign "Z" to gamepad 1, button 1, and assign "/" to gamepad 2, button 1... you can't do that. 2) I haven't found any emulators that make the rumble feature rumble (although I haven't really looked all that hard).
Keyboard/Mouse: Logitech cordless desktop. What amazes me is that the wireless keyboard, wireless mouse, and wireless gamepads all work fine together.
Kook