I believe you can encrypt everything except /boot, however if supported by your BIOS there's probably away to make your /boot partition a USB device. I don't have any good how-tos for you, because a lot changed with TrueCrypt 5.0, so the older tutorials are now out-dated.
Ignore HermanAB, who clearly has no idea what he's talking about. Encrypting / and /usr has advantages and disadvantages, and is most certainly not useless.
Lastly, I would encourage you to use dm-crypt and LUKS, unless you intend to view the disk on Windows as well. Not only will you find speed improvements, if you ever need to boot your disc from a live CD for recovery purposes, there are lots of distros that include dm-crypt and LUKS in the default install. If you use Truecrypt, you'd have to boot the LiveCD, download truecrypt and install it, then you could mount your partitions.
Obviously, this isn't my decision to make, but when I was looking at encrypting my laptop, I spent a lot of time trying to figure out how to do it with TrueCrypt, but eventually I realized there was a reason all of the tutorials use dm-crypt (and previously cryptoloop).