On your main company website, don't use the word "website" to refer to anything but the totality of the company's web presence. Specifically, don't use it to refer to subsites or departments. Using "website" to refer to parts of the site separates, rather than unites, your company's total offerings and it can confuse users, who naturally think that a different website means that they are going to a different company. For example, Ford's homepage uses an icon to mark links to external websites. However, Ford only uses this icon next to the link for its dealer finder, making it seem like it isn't part of the company. From the user's' perspective, of course, getting information about the cars and getting information about where to buy the cars are all parts of the same task.
If you offer web applications or services on separate websites, some users might go straight to a service website without going through the corporate homepage. It's fine to refer to those subsites as websites on the specific sites themselves, but from the corporate homepage it's better to present them as major categories. This portrays them as part of your total offering, rather than separate from it. For example, the Philip Morris website lists its subsidiaries, such as Kraft Foods International Inc., as part of its "Family of Companies," but doesn't label them as websites.