I personally go with encrypted disk images. You can create them in Disk Utility. You can then add the .DMG file to your login items to have it try to open at login. You can either have it save the password in your keychain, or have to enter it every time. If it's in your keychain, it's secured by your computer's login password, and someone resetting that password will not have access to the contents of your keychain.
I use this solution both here at work and at home. I also have symlinked my ssh keys to the disk image, because I make extensive use of remote access via terminal. It amazes me that apple has not rolled the ssh key folder into the keychain somehow yet.
If you haven't used them before, they work just like a flash drive. It's a fixed-capacity folder you can put folder, files, and other things into. Use is completely transparent once it's mounted up on your desktop, by double clicking the DMG and providing the password if necessary.
