I was interested in encrypting my dual boot laptop at the partition/disk 
level. I first tried Truecrypt but quickly found out it doesn't do this 
for the Linux root partition. LUKS seemed like the only reasonable Linux 
partition encryption solution, but again, it doesn't seem to address the 
root partition.

I ended up using Truecrypt to encrypt the Windows partition with 
pre-boot authentication. To boot to Linux, I bypass the Truecrypt 
bootloader to GRUB which boots Linux. Then I use a Truecrypt volume file 
in Linux.

Is there a better solution?

-Matt-