Step1
Remove the tank from the motorcycle, if necessary. Refer to the owner's manual on how to do this if you have one, if not, you can apply these basic techniques: Unhook any gas lines, or vacuum lines, depending on the brand of motorcycle. Some motorcycles are equipped with fuel valves on the gas tank. If yours has one, you'll need to remove it. Also remove the low fuel sensor, if your motorcycle has one.
Step2
Block all of the holes in the motorcycle tank. You can use a short piece of hose clamped onto the fittings on the tank, and closed off at the end with a bolt.
Step3
Dump the bag of BB's into the motorcycle gas tank and add the 1/2 gallon of diesel fuel. Shake the tank vigorously. The BB's will knock the rust, or any other debris, free and the diesel fuel will keep the particles suspended so that they will dump out.
Step4
Open the gas tank cap and look inside the tank. If it's not clean enough to suit you, resume shaking until the rust is removed to your satisfaction.
Step5
Pour out the diesel fuel and BB mixture. Shake the tank to make sure you have removed all of the BBs. Flush the inside of the tank out thoroughly with gasoline to remove all traces of the diesel fuel. Your tank should now be rust free and ready to put back on the motorcycle.

Things You'll Need:
Small bag of BB's
1/2 gallon diesel fuel
Gasoline

Here is a lot of discussion on this subject:

http://suzukisavage.com/cgi-bin/YaBB.pl?num=1267929971

I used tap water and bagged ice from the store.  I went through 3 bags doing this.

The first tankful looked like a red sludge.  It was easy to flush out with the garden hose.

I soaked the tank with distilled vinegar for 3 days after just to get it all.

I know I know, water???  Ice???  but it worked and was clean and easy.

I did a tank reconditioning write-up a while back for the Marauder group.  Still applies, mostly.  Check it out here... http://www.spacerjim.com/Fuel_System_Hygene.txt

Ignore the typos, and sarcasm.

You are correct, but it will only effect the surface.  You are not soaking the entire piece, only the surface and only for a very short time.  Essentially it will only dissolve the oxidised metal (rust), and then be removed.  Hence the instructions to use LOTS of water, and WD40.

But Phosphoric Acid may work, it just takes longer and more of it.  It is also known as Naval Jelly, "Behr Concrete Rust Stain Remover," "Kitchen Kleen Lime Gone," and Kano Labs ExRust.  (Check ingrediants before purchase in case they change them...)  The Naval Jelly will be harder to remove.

However, and this is a big "However..."  It does not remove rust, it converts it to black ferric phosphate. I do not know the effects of ferric phosphate to the fuel system.  And no one knows how it will react to whatever they decide to put in the fuel next year...  This is also why i do not use coatings like Kream.  The Muriatic acid will just leave bare metal.

I have moved this topic from the Tech Section to the Rubber Side Down.  The Tech Section is reserved for proven repair methods and this one seems to be open for debate and is not really a "HOW TO" that is universally agreed upon.  My own experience along this line began with putting drywall screws in the rusty tanks and shaking like mad......and you would be surprised how many drywall screws can get lodged into the narrow seams of the tank....and how long it takes to fish them out with a wire or magnet.

Later I tried Muratic Acid on a few tanks and it worked OK.......but it is not advisable to do this on a tank that has nice paint you want to keep.  Muratic acid is a very strong acid, it is used for cleaning the slopped mortar and stains off brick.  It comes in a gallon jug sealed in a plastic bag....and it is very concentrated.  It is darn nasty and should not be breathed or spilled.....however it is readily available at hardware stores.

Later I found out that Phosporic Acid is a better product for cleaning sheet metal.  Most metal prep products that are used to etch metal prior to painting are some form of Phosporic Acid.  It still can be harmful to paint.

My most recent find are products like Evaporust that dissolve rust and are completely safe to paint and your hands.  This product makes the rust fall off the steel and works great - but it is more expensive than the acids.  It can be used over and over until it wears out....then you can just throw it in your yard as it is a good fertilizer.

I also believe that once you have cleaned the tank - it is time to seal it to prevent future rust.  I have tried Kreem, Eastwoods product and now POR15 is my sealer of choice as it covers better and makes a nice steely grey tank color.....instead of a chalky white tank interior that the other products have.  

IF,, thats an IF there,, If my chemistry is right, when Ospho ( Phosphoric dilute) hits iron oxide, it spends its acidity when it turns the oxide to a phosphate. What little would be left in the tank should be rinsed out with plain water & the tank left to dry.

I was wrong.....or I just remembered wrong.

The product I used was Rusteco to remove rust from the tank of an old MG, and several motorcycle tanks.  It worked great.
http://www.rusteco.com/

I believe Evaporust is probably very similar:
http://www.evaporust.com/evaporust.html#Anchor_buy

And Zep is supposed to make a good product:
http://www.apmengineparts.com/m99535.html