I don't know any technical details about disk encryption except that
TrueCrypt is proprietary. I imagine that what Ubiquity sets up is secure.
When it comes to file encryption, as far as I'm aware, the most secure
methods of encryption are AES and OpenPGP. But I'm not sure.
This is the thing about encryption: if an encryption method doesn't work
well, current programs don't tend to recommend it. Other than using an
encryption method that works, what really matters isn't the method of
encryption, it's the key or password. If the key is weak, the encryption is
weak.
If you really want to be secure, you can combine multiple encryption schemes.
For example, start with a 7z archive protected by a password (this is AES
encryption) and then encrypt the resulting file with GnuPG.
