There are any number of ways in which the internet and e-commerce have changed the way companies do business. These changes vary with the kind of company involved.
For example, for many companies, the major impact has been the globalization that the internet makes possible. Thomas Friedman identified the internet as one of the major "flatteners" of the world because it allows for extremely easy communication and coordination between firms in different countries. Many firms have started to have much more globalized operations because of the internet.
For other firms, the changes have more of an impact on how they sell and/or deliver their products. A prime example of this is Netflix. This is a company that started out by mailing DVDs to people. Now, the advances in internet technology have made it so that the company does more streaming of content over the internet.