Here's a good article that shows how to do this with C++.
Next is my interpretation of it. Say, if your client-side JavaScript is:
function myMethod(name)
{
    alert("Hello " + name);
    return "Got it!";
}
You can call it as such:
CStringArray arrArgs;
arrArgs.Add(L"John Smith");
CComVariant varRes;
if(CallClientScript(L"myMethod", &arrArgs, &varRes))
{
    if(varRes.vt == VT_BSTR)
        AfxMessageBox(varRes.bstrVal);
}
Where the actual function that interfaces with IHTMLWindow2 is this:
BOOL CallClientScript(LPCTSTR pStrFuncName, CStringArray* pArrFuncArgs, CComVariant* pOutVarRes)
{
    //Call client function in HTML
    //'pStrFuncName' = client script function name
    //'pArrFuncArgs' = if not NULL, list of arguments
    //'pOutVarRes' = if not NULL, will receive the return value
    //RETURN:
    //      = TRUE if done
    BOOL bRes = FALSE;
    CComVariant vaResult;
    CComPtr<IHTMLDocument2> pIDoc2;
    if(SUCCEEDED(this->GetDHtmlDocument(&pIDoc2)))  //Uses CDHtmlDialog as 'this'
    {
        //Getting IDispatch for Java Script objects
        CComPtr<IDispatch> spScript;
        if(SUCCEEDED(pIDoc2->get_Script(&spScript)))
        {
            //Find dispid for given function in the object
            CComBSTR bstrMember(pStrFuncName);
            DISPID dispid = NULL;
            if(SUCCEEDED(spScript->GetIDsOfNames(IID_NULL, &bstrMember, 1, LOCALE_USER_DEFAULT, &dispid)))
            {
                const int arraySize = pArrFuncArgs ? pArrFuncArgs->GetSize() : 0;
                //Putting parameters  
                DISPPARAMS dispparams;
                memset(&dispparams, 0, sizeof dispparams);
                dispparams.cArgs      = arraySize;
                dispparams.rgvarg     = new VARIANT[dispparams.cArgs];
                dispparams.cNamedArgs = 0;
                for( int i = 0; i < arraySize; i++)
                {
                    CComBSTR bstr = pArrFuncArgs->GetAt(arraySize - 1 - i); // back reading
                    bstr.CopyTo(&dispparams.rgvarg[i].bstrVal);
                    dispparams.rgvarg[i].vt = VT_BSTR;
                }
                EXCEPINFO excepInfo;
                memset(&excepInfo, 0, sizeof excepInfo);
                UINT nArgErr = (UINT)-1;  // initialize to invalid arg
                //Call JavaScript function         
                if(SUCCEEDED(spScript->Invoke(dispid, IID_NULL, 0, DISPATCH_METHOD, &dispparams, &vaResult, &excepInfo, &nArgErr)))
                {
                    //Done!
                    bRes = TRUE;
                }
                //Free mem
                delete [] dispparams.rgvarg;
            }
        }
    }
    if(pOutVarRes)
        *pOutVarRes = vaResult;
    return bRes;
}