Before Microsoft started including whole-disk encryption in Windows (with Bitlocker in Vista), the best solution was TrueCrypt.
Now, according to its developers, TrueCrypt is no longer secure and should not be used. Development has been shut down and users are being instructed to use something else.
There is a lot of speculation about what’s going on. Recent revelations about security solutions being compromised by the NSA led one group to undertake a complete audit of TrueCrypt. It’s not much of a stretch to imagine that this audit prompted TrueCrypt’s shutdown. If the NSA inserted a back door into TrueCrypt, the software’s developers might want to keep that a secret. On the other hand, the audit continues, regardless of TrueCrypt’s status.
Anyone using TrueCrypt is strongly encouraged to switch to something else, like Bitlocker.