There are a few options.
Most versions of Linux offer a way to encrypt home directories during install. This stores the filesystem encrypted on disk and then decrypts when the files are needed. This adds overhead and can potentially impact performance, of course.
If you just have a certain file or directory you want to keep secret, you can use symmetric encryption with gpg. I periodically tar up big directories, encrypt them with gpg, and then upload them to a backup archive. You just have to remember the password(s).