A lot of front ends give you the option to hide clones.
I'm pretty sure that the main rom (non-clone) is usually the last US or world release.
This is how I do it, but there are a few exceptions.
Pacman is a clone of Puckman, so I go into the mame.xml and change it to trick the front end.
Sometimes on four player games like the simpsons or teenage mutant ninja turtles, you don't have the ability to select your character.
It is assigned to you based on which player you are. Using the 2 player version of these games works out better on a 1 or 2 player cab and allows you to choose which character you want to play as.
I've read that fairly often the US release of a game will be more difficult or even impossible for the sake of taking your quarters and the Japanese version will be more balanced and enjoyable. Can't say I've ever given them a try though. I grew up on the quarter stealers and that's what I want.
EDIT:
To research a rom, I use:
http://www.progettoemma.net/(click the combo British/US flag above the search fields for English)