How to efficently use Drupal as a laboratory notebook and information management system?
How do you want to organize your information?  I would use a content type such as 'notebook_entry' with a taxonomy 'subjects' and/or 'projects' that allows free tagging of terms.

notebook_entry should use the body field for the bulk of your content.  You can add additional text/image/file fields for storing related information that can be displayed with the content.

I recommend using views to display your notebook entries.  You can create an argument in your page view with the taxonomy term or terms you've defined for the notebook_entry content type.  This will make the page only display entries related to that term.  You'll have to create a menu block filtered by the taxonomy to access your content.  It will list each of the taxonomy terms as links to your page view that displays your notebook_entries.  Create a list of terms and use the global text field to make a link to the path of your page view including the arguments.