Last time I used Fedora (this was Fedora 9, YMMV), I had everything encrypted with LUKS and cryptsetup in a ext3 volume in my lvm volumes, and it did this quite well. If you want a bootable system with encrypted data hidden until a user opts to mount the right container (instead of blocking the boot process at the sake of preventing any unauthorized use like what I propose), the TrueCrypt solution mentioned above might be better. Anaconda (the Fedora installer) asked if I wanted it back then, and I tried it out of curiosity. I even hosed that laptop ages ago, and was still able to recover the data with a bootable Linux disk, so command fu, and remembering the key of course. TrueCrypt is also very well-tested, and has tons of cool features.