I'm thinking of setting up a file server with JBOD (just a bunch of disks). Is it possible to encrypt the entire array of concatenated disks with TrueCrypt and what happens when I need to replace/upgrade an individual drive?
This is a very bad idea to do with JBOD. If you lose a single disk, you will not be able to recover any of your data. I would recommend at minimum mirroring if you have more than one disk to throw around. Encrypting the drive in that configuration should be pretty safe as long as you keep the keys to the encryption straight.