There are a variety of tools that offer encrypted filesystems for the various OSs. None of them are as easy to use as we would like, and none have reached the goal of "Zero User Interface" (ZUI) that is the only thing which causes successful deployment of encryption (ie. Skype, SSH and SSL.)
Many of these tools have a risk of failure if you don't also encrypt your swap/paging space, because your swap file will contain fragments of memory, including encrypted files and even in some cases decryption keys. There is a lot of other confidential data which can end up in swap -- web banking passwords and just about anything else.
It's not too hard to encrypt your swap on linux, and the ecryptfs tools package includes a tool to set up encrypted swap (which is not done with ecryptfs, but rather with dm-crypt, the block-device encryptor, but it sets it up for you.)
However, I would propose that swap be encrypted by default, even if the user does nothing. When you boot, the system would generate a random key for that session, and use it to encrypt all writes and reads to the swap space. That key of course would never be swapped out, and furthermore, the kernel could even try to move it around in memory to avoid the attacks the EFF recently demonstrated where the RAM of a computer that's been turned off for a short time is still frequently readable. (In the future, computers will probably come with special small blocks of RAM in which to store keys which are guaranteed -- as much as that's possible -- to be wiped in a power failure, and also hard to access.)
The automatic encryption of swap does bring up a couple of issues. First of all, it's not secure with hibernation, where your computer is suspended to disk. Indeed, to make hibernation work, you would have to save the key at the start of the hibernation file. Hibernation would thus eliminate all security on the data -- but this is no worse than the situation today, where all swap is insecure. And many people never hibernate.