I think it mostly depends on whether you it is an horizontal or vertical game, and which aspect ratio you which for it to run at.
If you're developing for a 4:3 monitor, then I think 320x240 or 640x480 would be best. The difference mostly comes down to how much detailed you want it to be; that is, a 320x240 game scaled by two will occupy the same resolution as 640x480, so the only difference would be whether you want to draw the sprites at native 640x480, or to scale the ones drawn at 320x240.
I'm pretty certain that many, if not most, of those resolution would be scaled to 4:3 on an actual cabinet (some missing a few scanlines on the top/bottom, others on the left/right, etc), so all those different resolutions can be a little misleading. For example, 256x224 is NES NTSC resolution, and 256x240 is NES PAL resolution.
Similar with 16:9 resolutions; for example, 1280x720 or 640x360 (or similar; depends on whether you want the game to occupy the entire screen, because then you'd want to use a resolution that the monitor supports natively. Might support one lower than 1280x720, but I'm not certain).
And, if I'm not mistaken, Daioujou, for example, has a native aspect ratio of 2:1, but is scaled to 4:3 on an actual cabinet.
Of course, the actual playing area of the game doesn't have to be the same as the monitor's aspect ratio (unless you're going with an horizontal game, and you want it to occupy the whole screen, or you're going with a vertical game on a vertical monitor (3:4), again, also occupying the whole screen). Some games use a nearly square playing area, like ChoRenSha (don't know if it's actual square, but it's close).
You might want to play around with them a bit, and see what you think feels the best.
