TimeMachine is a backup system working out-of-box on OS X, supports encryption and is quite easy to setup. Backing up is only a half of the deal though; you may need to restore it some day. You can restore the whole system on a new Mac, and it’s also possible to get the individual files if the need arises.
You can mount your external disk or TimeCapsule backup as another volume. In case of TimeCapsule, you connect to your WiFi router, go to Data/, and mount an image with the name like my_mbp.sparsebundle (for encrypted backups, OS X creates an encrypted sparse bundle which can be stored on any filesystem), where my_mbp is your computer’s name.
Then on your mounted volume, you’ll see the Backups.backupdb/ directory, inside a directory with the name of your computer (say, my_mbp/), then timestamp-named directories with different backups. So restoring some files should be as easy as:
$ ls -le ~/Desktop/OCMock.framework
total 48lrwxr-xr-x 1 user staff 24 Jun 1421:47 Headers -> Versions/Current/Headers
-rw-r--r-- 1 user staff 10174 Jun 1421:47 License.txt
lrwxr-xr-x 1 user staff 23 Jun 1421:47 OCMock -> Versions/Current/OCMock
lrwxr-xr-x 1 user staff 26 Jun 1421:47 Resources -> Versions/Current/Resources
drwxr-xr-x 4 user staff 136 Jun 1421:47 Versions