While Java is a cross-platform programming language used to create applications, a Java applet is a program that can be embedded in other applications (such as a web browser), which is typically the way we experience it on a web page. Java applets are a completely self-contained area of a web page, separated from the rest of the page much like a Flash embed.
Search engines do not crawl or index content found in Java applets. Therefore, it's important that no content that you would like to have appear in search engines is placed in a Java applet. For usability, SEO, security, and other factors, it is generally a best practice to minimize the use of Java applets on websites whenever possible.