If you want a graphical interface that integrates well with gnome, try cryptkeeper.
The home page is here : http://tom.noflag.org.uk/cryptkeeper.html
It is in the ubuntu repositories.
Other options include Truecrypt, ecryptfs, and LUKS.
ecryptfs is also in the ubuntu repository,and should be installed by default, If it is not:
sudo apt-get install ecryptfs-utils
Make an encrypted directory, to be decrytped when you log in with
To make a directory that is not automatically decrypted when you log in you will need root access
chmod 700 secret
Encrypt the directory
sudo mount -t ecryptfs ~your_user/secret ~your_user/secret
You will be asked to enter a passphrase and a number of additional questions. Go with the defaults (hit enter) but answer y (yes) to "Enable filename encryption (y/n) [n]:" to encrypt file names.
Place any data you wish encrypted in ~/secret .
To encrypt the data
sudo umount ./secret
To decrypt the data, mount the directory again
To make it easier you can give the options you desire to the mount command with the -o flag (all one line)
sudo mount ~your_user/secret~your_user/secret -o key=passphrase,ecryptfs_cipher=aes,ecryptfs_key_bytes=16,ecryptfs_passthrough=no,ecryptfs_enable_filename_crypto=yes
Either make an alias in ~/.bashrc or make a custom launcher.