zack: Any testing done? Stool tests are hit or miss, the best test at the moment is the Metametrix GI Effects - use panel #2105 to save money.
If you don't know what it is then you will have to rule things out - if you suspect worms then look at some of the formulas (personally I am not a fan of the Clark type of supps -black walnut etc)., Banyan Botanicals has a nice formula - I got roundworm out using neem, boswellia, myrrh and enteric coated oil of oregano (NOW) - I knew someone who got toxocara out using the protocol for Lyme - salt & vitamin C.
There are a number of protozoa that can cause problems as well, other suspects would be flukes. Have you looked at ICU's protocols she posted?