One of the greatest advantage of Drupal is that it is extremely flexible. This leave to the developer lot of freedom on how to implement the solution. Basically there are lot of different ways to achieve the same goal. The best ways to use Drupal is to set up an architecture that will be scalable for your application. The best approach is to set up a different content types or entities, one for each specific real entity. You can cross reference entities using entity reference so do not create only one entity that host the whole application data, but create relations between small entities so that data is stored efficiently and it will be easier to scale and it will have higher performance. If you need to display aggregated information you can use views to JOIN multiple entities.
Set up content types, taxonomies and blocks. Classify and group your content using taxonomies and views. Views helps to group the content in a different sections such as latest news, featured articles, services and all necessary website widgets.
Plan your strategy to use Drupal at the best of its capability and performance. As Drupal is written in PHP it requires that a module is loaded when needed, therefore it is highly recommended to install a module only if it is really necessary. Decide in advance which modules to use in your project.
Integrate Drupal with other systems using the web services API module. They can be used for reading feeds, exchange data between complex systems which generally produce Jason or XML files.