Almost all email clients and anti-virus programs strip out or block JavaScript as a security measure to prevent viruses. This is also true for other code and plug-ins such as ActiveX, PDF, Forms and Flash. After the data is stripped or blocked, the email will look different than originally intended. To avoid the email from being changed by the email client, do not include these customizations in your custom HTML email, instead save them for your website.
You can always add a text link or an image (.png or .jpg format) in your email and provide the link to where the other code or plug-in resides, whether it be your website or another site you host data on.