I Have a few suggestions but no definitive best go to solution since it really depends on your specific use case.
First off look into BerryBoot, it offers full disk encryption out of the box.
A second alternative is to use any of the TrueCrypt like applications such as VeraCrypt It offers a bunch of options to either perform full disk encryption or make sure that specific vulnerable files are safely encrypted.
A third option, similar to the second is encrypting directories on the disk
If you are more technically inclined and would like to manually perform certain taks it is also possible to use LUKS/dm-crypt yourself.
You will have to keep certain things in mind though: The computational power of the Pi is limited so any form of encryption on the devices will cause a performance hit.
Secondly you will have the problem that you will need to manually enter the key each time the device wants to perform an operation, since storing it in a physical form on the device makes it vulnerable to anyone with physical access.