For more tips on how the NSA locks down its OS X machines check out "How the NSA snoop-proofs its Macs."
Linux encryption options
For Linux users, the best choice is to use a distribution with a built-in Linux Unified Key Setup (LUKS) implementation. Ubuntu uses LUKS, and the various distributions based on Ubuntu should all have full disk encryption options available during installation. Here's how to get started with Ubuntu's full-disk encryption, courtesy of Ubuntu's community help documentation.
It's a sad day if TrueCrypt has truly disappeared, but at least there are a number of alternatives open to users who need or want to continue encrypting their stuff.
Sign up for CIO Asia eNewsletters.