If you play horizontal games (Neo Geo, etc) as well as vertical games(pacman) and special resolution games (all midway games - MK, NBA Jam, etc) then you need to figure out which one is the most important for you and stick with it.
For me, the most important is standard resolution horizontal games. In this case, pacman and midway games get cut at the top and bottom. Lots of threads here about it.
To fix this, you'll need to run those games with hardware streatching enabled. The game will look full screen, but you'll notice interlacing in those games.
i.e. My resolution of choice is as follows: (Mind you, we're stuck doing stuff like this because, unlike regular PC monitors, arcade monitors can't easily on the fly switch resolution and fix holds at the same time! they weren't made for that!)
Windows XP - 640x480 interlaced
horizontal games-

x 240 resolution non interlaced
vertical + midway - 640x480 HW streatched interlaced
Notice how in all 3 cases it's the same resolution??? 480 interlaced = 240 non interlaced!
Hence vertical hold doesn't need to be ever adjusted and I can play the most amount of games!
Hope this helps.