Well, that's a tough question to answer. Not only do you have uprights like capcom bowling that were cocktail with screen fliping, you also have dedicated cocktail games like atari football.
Most people setup up their coctail with controls opposite each other on the virtical side. Then have 2 players side by side on the horizontal side. That should cover most everything. It'd take alot of money and some work to actually have 4 trackballs for games like atari football and atari soccer and 4 spinners for games likw warlords. So you might not catch all games to their fullest potential.
Now, my plan for my cocktail is removable control panels. They will have have a single USB cord coming out of them. So, say I have player 1 controls. I can then detacht he controls, unplug the USB from the vertical side and move it to the horizonal side. I am going to design it so it looks better when the controls are on the vertical side as there re not that many horizontal cocktail games, especially ones where players would sit across from each other. Space duel did but it can be played with players on both sides. I have my upright cabinet to two player games on the "same side". Actually thinking about it, my cocktail cab may only be vertical...