My home folder is already encrypted.
One thing I do not understand is how to make a walletpassphrase on linux. On windows you have the option setting - encrypt wallet. I did not find the same option on linux. Anyone can tell me how this is done ?
I am running xubuntu 13.04 running bitcoin-qt, there should be the option in the window under one of the menus. I don't have bitcoin-qt setup at the moment as my HDD fried earlier today, but once I do I'll reply with some pictures.
Also, you can always use the API to do it, but thats a bit more involved.
Edit: Also, to avoid situations like mine (I did this luckily), after encrypting the wallet.dat I would make an archive that is encrypted and store it on a USB/online service. This way if your HDD does fry you don't lose you bitcoins