For external/data disks, TrueCrypt is the software of choice. Others may match or even exceed its functionality, but none are as thoroughly examined.
For system disks, my current favorite is BestCrypt Volume Encryption. It is expensive, especially if you live in EU, but has the best mix of functionality and ease of use of all programs - and unlike some competing commercial software, it doesn't have annoying antipiracy measures.
If you want free system encryption, DiskCryptor seems to be a good choice, except that as far as I can tell, it's developed by only one developer.