Since you put this in Windows on the Mac, are you talking about encrypting a Mac disk, a Windows disk, both, neither? And if Windows, XP or Vista?
On the Mac side, people have traditionally eschewed FDE in favor of Filevault, which only encrypts the home directory and (separately) the swap, since this is generally considered sufficient. I use Filevault. Just make sure you do full disk clone backups. It's very satisfactory to me. Truecrypt is available, though. Thread about that
here.
On the Windows side, I don't have much to add; Truecrypt is generally the top recommendation in XP, but I don't know about any special considerations when using it in Windows on a Mac.