If you're serious about protecting PDFs and stuff, encrypt them with PGP. It's much more annoying than using FDE systems like Truecrypt, but much more secure.
If you're not so serious that you're willing to manually encrypt and decrypt files (or ZIP archives of files), just use your OS's full disk encryption scheme. On a Mac, for instance, you can create virtual disks with AES-XTS and keys derived from passwords; that's built into the OS.
What people really want is some kind of transparent encrypted filesystem. That's a reasonable thing to want, and it would be more secure than Truecrypt. I don't know of a good one.
