Using multiple partitions you could also use TrueCrypt, though I don't know if full disk encryption on Linux works the same as in Windows or at all. Both TrueCrypt and dm-crypt/LUKS (using LVM) have proven themselves for security, though TrueCrypt includes hidden containers (plausible deniability) and dm-crypt/LUKS can use more encryption algorithms (might equal better protection). I know TrueCrypt can store the headers of the encrypted disk on a rescue volume in case the hard-disk gets corrupted. I don't know how or if dm-crypt/LUKS include those. It's a matter of personal choice really.
If you encrypt your home partition, but not the rest, you could leak data to the other partitions when running the OS, so don't do that unless you know what you're doing. Usually it's best to go all or nothing.
Free your mind / Think clearly