Back and forth speculation is great and all, but does anyone know of a solid alternative to TrueCrypt? Perferably open-source but at the very least not a potential government lap-dog like Microsoft?
Wild guess here but you might want to recreate any containers using tcplay and copy files over, rather than continuing to use possibly compromised truecrypt containers.
For full-disk encryption Linux has LUKS/dm-crypt/cryptsetup.