Having these elements on your page is not necessarily bad. For example, the Traffic Analyzer will add a small amount of Java to the bottom of each page you specify to add visitor tracking. This should not hurt your rankings. However, if you have a large amount of Java, VBScript, or ActiveX control code at the top of the page, this can end up diluting the prominence of your keywords, and thereby the effectiveness of your page in terms of how it ranks. Therefore, at least for your doorway pages, try and keep things simple and minimize unnecessary scripting and coding.