With EndNote X4 and above it is possible to import a PDF or folder of PDF's into EndNote, and EndNote will attempt to pull metadata from the PDF to create a reference automatically.  

The quality and amount of data that EndNote can pull out from the file is dependent on the individual PDF.  On some occasions a complete record is generated and sometimes a very sparse record will be created - either way more data can be manually inputted.

How to Import a PDF:

File -> Import -> File.  You will be asked to find the file using the Choose button. You will need to change the Import Option within the window to be PDF.

Alternatively, multiple PDF files can be added at the same time by navigating to File -> Import -> Folder and locating the file in which your PDF files are stored. As above, you will need to ensure that the Import Option is set to PDF.

It is worth noting that EndNote X5 has some new features that are designed to make adding additional reference information easier, and will help you complete the reference if EndNote can't do it from the PDF.

Once the new reference has been created with the PDF attached you can go to the PDF + Quick Edit tab at the bottom of the EndNote screen and use the copy and paste features to insert reference information into the correct fields.  

An additional new feature that can be used to compile the reference is the Find Reference Updates feature, which can be found via the References menu at the top of the screen. When using this feature EndNote will try to find more details from the internet to complete the reference.  This will work best if the Author, Year, Title and DOI fields contain reference data.

Also note that for X6 you can drag PDFs into EndNote's toolbar area to initiate the Import PDF tool, see the attached short movie.