There has been much discussion over Multi-Classing in C&C of late, even more so since the release of the 4th printing PHB into the wild.
As there are rules for it in the current PHB you would think it would end, but the debate continues.
I (for one) still prefer the original AD&D way of doing, and restrict multi-classing to non-human characters and dual classing to human characters. Not just for old times sake, but because it makes Humans too powerful and desirable as a character race at the expense of the non-human races.
Of course then you run into the brick wall that is the fact that non-human characters can only have two prime attributes, and that its a requirement to have the prime attribute of a class as one of your primes - thereby restricting your non-human character to multi-classing in just two classes.
One of the options I use is based upon the way we do attributes (Primary/Secondary/Tertiary).
If a multi-class option is taken, and the prime attribute for that class is a secondary attribute - then a 10% tithe is placed upon all EEP (or XP) that is applied to that class (so deduct 10% before applying it to your EPP (XP) total for that class) - if a multi-class option is taken, and the prime attribute for that class is a tertiary attribute - then a 25% tithe is placed upon all EEP (or XP) that is applied to that class (so deduct 25% before applying it to your EPP (XP) total for that class).
Now the 25% penalty might seem harsh, but its there for a reason - to DISCOURAGE a player from taking a Class with a tertiary attribute - JUST BECAUSE HE (OR SHE) can - we've all encountered such discommodious players.