Determine if file or directory is encrypted?
If you're using FileVault 2 (OS X Lion and newer), the entire boot partition will be encrypted, which includes your home folder as well as Applications.

I ran the following command and part of the output shows I am using an encrypted, unlocked volume:

ashley@sidekick-4:~$ sudo diskutil list
/dev/disk0
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *251.0 GB   disk0
   1:                        EFI EFI                     209.7 MB   disk0s1
   2:          Apple_CoreStorage                         250.1 GB   disk0s2
   3:                 Apple_Boot Recovery HD             650.0 MB   disk0s3
/dev/disk1
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                  Apple_HFS Macintosh HD           *249.8 GB   disk1
                                 Logical Volume on disk0s2
                                 2DDC5CBD-1B65-403E-9D4F-9424BC764433
                                 Unlocked Encrypted
/dev/disk3
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *2.0 TB     disk3
   1:                        EFI EFI                     209.7 MB   disk3s1
   2:                  Apple_HFS Time Machine Backups    2.0 TB     disk3s2
ashley@sidekick-4:~$