2014-05-28: TrueCrypt currently has security issues and is not recommended.
If you’re running GNU/Linux, dm-crypt with LUKS is the recommended encryption option.
Gentoo GNU/Linux maintains a guide for dm-crypt with LUKS.
Arch GNU/Linux maintains a guide to dm-crypt with LUKS. Also useable for Parabola GNU/Linux.
Slackware Linux maintains a guide to dm-crypt with LUKS.
Transparency in this context means that individual programs don't need to manage encryption of their own data, because this is provided equally for all programs by the encryption tool (like dm-crypt). More details on this in the Wikipedia.