The the following folders are recommended to be encrypted:

• Encrypt the Documents library if you save most of your documents there. Encrypting this folder ensures that any personal documents saved there are automatically encrypted. However, a better alternative would be to create a subfolder under Documents library for personal files and encrypt just this folder. This approach relieves you from having to track which files are encrypted and which are not.
• Encrypt your Temp folder so that any temporary files created by programs are automatically encrypted.