Well, to be comically obvious... if a story has a teenage Clark who's friends (sort-of) with Lex, who has a best pal named Chloe, and a history of dealing with "meteor freaks" then it's probably not L&C.
But it'd be darn near impossible to set down specific guidelines (you can use Lex, you can't have Chloe, etc). So we rely on people's good sense in general, and look at specific cases as they come up. <shrug> Can't really get more specific than that; it's not always black-and-white.
PJ
who, btw, would enjoy a good Smallville Clark&Chloe shipper fic if anyone has any recommendations...