Curt Sampson did a great job explaining the concepts. I'm gonna give some details.
Sadly, Seahorse & friends doesn't give the option to do symmetric encryption yet, though it can handle decrypting symmetrically-encrypted files. In the meantime, as has been said, you can do your encrypting from the commandline, e.g.
gpg --symmetric --force-mdc --cipher-algo aes256 -o outfile infile
If you're happy with gpg but really want a gui, you could use my gpg-frontend Pyrite. It doesn't integrate with Nautilus like seahorse-plugins, but it's still pretty sweet, if I may say so. :)
As someone else mentioned, eCryptfs is a great option that sorta falls into this same realm, providing per-file encryption, though it does it in a much more convenient way, basically providing you a folder that transparently encrypts/decrypts all writes & reads to/from it. At first it seems like an encrypted container solution, but really it's encrypting the files individually -- once you unmount the folder, you end up with a bunch of singly-encrypted files. This article at LJ gives a good compare & contrast overview of eCryptfs vs some of the other options. Here's how simple it is to get eCryptfs going:
$ mkdir ~/vault
$ sudo mount -t ecryptfs ~/vault ~/vault
Select key type to use for newly created files:
1) openssl
2) passphrase
3) pkcs11-helper
4) tspi
Selection: 2
....... (truncated)
$ echo hello > ~/vault/encfile
$ sudo umount ~/vault
$ ls -a ~/vault
. .. encfile
$ cat ~/vault/encfile
稖��)!x�"3DUfw`��ȿ_���E�����_CONSOLE�W�v0�+�'�hV���Q��VZ��eP�����l⟮j%����?O��V
....... (truncated)
If you're interested in this, also checkout the ecryptfs-setup-private
command which eliminates the need for sudo and allows automating everything. Moving on.
The best other options are the ones mentioned by pts: TrueCrypt (which is cross-platform) and dm-crypt, which allows you to encrypt any block-device (e.g. partitions, logical volumes, single files) and then of course you throw a fs on top of that. Don't use Cryptoloop (predecessor to dm-crypt).
I mostly only have experience with Red Hat, Fedora, & friends, but in those you can use the lovely disk management gui palimpset
to create and modify encrypted disks/partitions right out of the gate without installing anything extra. Of course there's a command-line util for this: cryptsetup
... here's a simple example to give you an idea of what's possible with dm-crypt, using cryptsetup to make an encrypted filesystem out of an extendable logical volume:
lvcreate -L 2G -n mybox volgroup
cryptsetup luksFormat /dev/volgroup/mybox
cryptsetup luksOpen /dev/volgroup/mybox mybox
mkfs.ext4 /dev/mapper/mybox
cryptsetup luksClose mybox
Once you've done that, Nautilus should have no trouble auto-detecting it and then you can unlock it and do a secure user-mount from there.
EDIT: I feel silly. I was browsing through gpg tags when I came across this question. I didn't notice how old this was until I finished typing everything and was about submit it. Oh well. Perhaps it will come in handy for posterity.