All sorts of CS problems. The class name should be Math_BigInteger, all of the defines should be MATH_BIGINTEGER_FOO, etc.The documentation, while thorough, needs to be in the phpDocumentor format. Also, the header isn't the required PEAR header.
The bcpowmod function you define should either be a part of PHPCompat (ie. your package requires PHPCompat, which implements this function) or you should put that if statement into your class definition.
Ideally, your class would use the native BC functions if they existed as well.