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I wrote most of this guide a while back, and decided to finally finish it. The main goal here is to have a relatively simple way of creating a secure offline wallet entirely in your control. The methodology below avoids having to install additional software or download the whole blockchain to a dedicated offline computer (which is required with some offline storage methods). After practicing a few times, the steps below can be executed from scratch in 15-30 minutes.

Please let me know if you have feedback on how to make it better! Also, I highly recommend trying the whole process several times with small amounts until you are comfortable with it and understand all of the steps.

Creating a secure offline bitcoin wallet

Step 0:
This is step is for brain wallets only.

Spend some time thinking of a secure, memorable passphrase.
The passphrase MUST BE something unique to you with at least 8 words. DO NOT USE something from a book, movie, poem, etc.
Basically, if the passphrase can be found in (or easily generated from) any existing media, your funds will be at risk.

An example of a decent passphrase formula:
[your mother's birthday multiplied by your favorite number] +
[every other word of some obscure phrase that holds special meaning to you] +
[your home phone number when you were a kid] +
[the first 5 words of your best freshman year english paper, ASSUMING IT ISN'T SEARCHABLE ONLINE]

You should save clues to this passphrase that are only helpful to you in several safe places.
Also practice regenerating the private key using the passphrase on a regular basis (every month or so), just to make sure the phrase stays fresh in your mind.
Step 1:
Buy two USB sticks.
Step 2:
Download ubuntu desktop ISO (12.04 is current Long-term supported version, at the time of this writing)
http://www.ubuntu.com/download/desktop
Step 3:
Download a USB linux installer.
http://www.pendrivelinux.com/universal-usb-installer-easy-as-1-2-3/
Step 4:
Plug in brand new USB, and run the USB linux installer program (from step 3) to install a fresh copy of linux OS on the USB drive.
Select the linux version matching the iso you downloaded, press create (see pendrivelinux.com instructions).
Step 5:
Save the bitaddress.org webpage to the second USB (or to your desktop).
Step 6:
THIS IS VERY IMPORTANT: Make sure networking/internet is completely off/disconnected.
Turn off PC, and then re-boot from linux OS on your USB.
To do this, I had to press the f2 during system load screen (specific key may differ by manufacturer).
Step 7:
Locate your offline copy of bitaddress.org (from second USB or harddrive).

If creating a brainwallet, then go to the brainwallet tab, and input your secure passphrase to generate your new private/public key.
Quadruple check for typos and correctness. Record the public key(s) and save them in a few places.
You can start by copying the new public addresses to a text file on your second USB.
You do not need to keep the public keys private, unless you don't want people knowing what address has your coins.

If creating a paper wallet, then navigate to the paper wallet tab. Print out as many paper wallets as you need.
I recommend make a few copies of each and storing them safe places (locked, fireproof safe in your closet, parent's house, bank deposit box, etc).

NOTE: you may wish to repeat this step several times, so that when accessing/redeeming a savings wallet only part of yovery,avings are at hand, and you do not have to repeat the offline wallet creation process.
In a perfect world, you shouldn't re-use a long term savings address that has been spent from.
Step 8:
Fully wipe the USB stick. This isn't 100% necessary, but if you are feeling extra paranoid, it won't hurt. The main drawback to doing this is that you then must re-install linux onto the USB (step 4).

Securely spending your offline funds

Step 1:
See steps 1-4 above.
Step 2:
In addition to bitaddress.org, save a local copy of brainwallet.org to your second USB or hard drive.
Step 3:
Save to your extra USB (or hard drive) the receiving address that you wish to send your saved funds to.
Step 4:
Retreive transaction history for your savings address by replacing [YOUR_ADDRESS] in the following URL with your actual public key:
http://blockexplorer.com/q/mytransactions/[YOUR_ADDRESS]
Copy the transaction history (text on the page from above URL) to a text file and save to your extra USB.
Step 5:
THIS IS VERY IMPORTANT: Make sure networking/internet is completely off/disconnected.
Turn off PC, and then re-boot from linux OS on your USB.
To do this, I had to press the f2 during system load screen (specific key may differ by manufacturer).
Step 6:
Open offline copy of bitaddress.org
Type in your memorized passphrase on the brainwallet tab to retrieve your private key.
Copy this and close the page.
Paper wallets can skip this step, simply type in the private key from your paper wallet.
Step 7:
Open offline copy of brainwallet.org, and navigate to transaction tab.
Paste your private key into the correct field (labeled private key).
Paste the receiving address (public key) you wish to send funds to into the destination address field.
Open the text file containing the transaction history for your savings address that you are spending from.
On the brainwallet.org page, click "edit input" and paste in the transaction history.
Right above, it should say "Use history from" and give two options. Choose "Bitocin block explorer".
The page should use the transaction history to figure out how much BTC you have available in your savings address.
Double check this value. Then, input how much you want to send to the receiving address.
Click the + button to add an additional receiving address.
Take the left over coins (the "change"), subract a small fee and send that amount to a brand new savings address you have created.
If you want, you can send the leftover amount back to the original address, but this is a tiny bit less secure (and reduces privacy).
Input the small fee into the fee field. Triple check everything.
If it looks good, click "re-sign" transaction and copy all the text in "raw transaction" field into a text file, and save this to your second USB.
It is ok if someone sees this raw transaction data, they cannot steal your private key from it.
Step 8:
Turn off computer, remove the USB that has linux on it. Reboot to your normal OS, and reconnect to the net.
Open the website https://blockchain.info/pushtx.
Copy the "raw transaction" data from previous step into the big text field, and hit "submit transaction".
Your funds are now on their way! You can track them by exploring your address with blockchain.info search.

Notes

I very, very strongly recommend doing both processes listed above at least 2 or 3 times with SMALL amounts of bitcoin that you are comfortable losing. Do this until it all makes sense, and you understand what is going on.
Then feel free to make you actual savings wallet! =)