My preference is to encrypt entire drives and partitions, which is the level at which I organize my data these days, and that's exactly what DiskCryptor does--even with your system partition. The program takes that one further and will encrypt ISO files that you may then burn to CD. If you need encrypted container files, look to TrueCrypt or others. See all Software reviews.
You can encrypt entire drives with DiskCryptor, which runs as a service and is configured via a dialog. It also works in Windows 8 desktop mode.
After you install DiskCryptor, it runs as a service in the background with an icon in the system tray. You can set it up to load from your boot sector if you've encrypted your system drive. Click on the system tray icon and you're presented with a plain, down-to-business dialog from which you encrypt/decrypt (AES 256, Two-fish, Serpent) as well as mount and unmount encrypted drives. The program uses only a little over 1MB of disk space installed.
There are a few peculiarities with DiskCryptor that you should be aware of. When you unmount an encrypted drive, it's still visible to the system, as well as Windows Disk management, but isn't recognized as a validly formatted or partitioned drive. This could lead someone to think the drive is corrupt and repartition or reformat it.
A hide drive function would be nice. Also, it would be nice to have context menu support so you don't have to go through the dialog for everything. But that's a lot of complaining for a program that's free, easy, convenient, and works extremely well.
DiskCryptor encrypts at the sector, not file level, so converting a drive one way or the other can take a while. In my hands-on, the program worked perfectly and encrypted a 64GB USB 3.0 flash drive in about 20 minutes, or 50MBps on a fast Core i7 system. Decrypting was considerably slower at about 20MBps. Copying files to the flash drive proceeded at about 55MBps--encrypted or not.