You can place a Google doc, presentation, spreadsheet, or any file into a folder from within the document using the folder icon next to the file name.
Google Drive makes using folders a lot more logical. The ability to sync specific folders to your computer and add them to My Drive puts organisation back on the menu. Yes, you can still rely on the powerful search facility to find a document, but you now have a reason to organise your files into folders in Google Docs.
So, if you have decided to start (or continue) organising your files into folders in Google Docs, you can do this from within any open file. Click on the folder icon and a dropdown box will open showing you which folders (if any) the open file belongs to, you can click the Organise button to open up the standard Organise box.
You can also star a file or document using the star icon next to the folder icon, 2 handy ways to organise your open files.
TIP UPDATE: The Organise button has been moved to the File menu. To organise from within a document, click on File and choose Move to folder... from there you will see where the file currently is in your Drive and can choose any number of folders the file can be located in (just remember to keep Ctrl pressed down as you click your mouse!)