When you use HTML module, you can't have Javascript or CSS to link a js or css file.
Normal solution is to save a seperate file under Documents, and use Iframe to link the file.
IFrame Generator is free tool, allow you to generate a code use it in a HTML module. It is one step solution.
It is easy to use, just copy your 3rd party code, like Google adsense or eBay or etc, into "Your html/script code", click "Generate Code" button and copy&paste generated code into your HTML module.
You can use it for Google adsense, Google Reader, RSS feed, Ticker, eBay market feed, Paypal, Google Checkout and etc.