Nothing

Boringly, nothing much would happen. The only way carrying helium-3 would really matter in an explosion is if a weapon impacting the helium were powerful enough to induce fusion. A nuke might do it, but if the weapon is that powerful to begin with, then the additional explosiveness is not going to be particularly noticeable.

If the fusion reactor just happens to lose containment, then all that will happen is the plasma will melt the reactor wall. If it's not caught in time, then it will melt the magnets too. At that point the plasma will escape, and then... the plasma will rapidly cool. Without the magnets to contain the plasma, the gas cannot reach the fusion state, so there is no explosion if there is a reactor breach.

I think the solution are the anti-gravity drives. What if putting them out of balance while still powered causes them to create intense gravitational gradients? Gradients so steep that they create visual gravitational lensing, so intense that the gradient crushes the saucer's hull like a soda can, turning the crew to red jam, and causing a flash of light at the focal point of the gradient. The saucer would also spin out of control. The gravity drive would completely shatter and explode from this, with the rest of the ship quickly break apart n the process. So, no bang, but a crack, suck, crunch, and wild uncontrolled spinning all in less than a second! Gravity my friends, gravity is the answer.

Fiery Helium

Just some off the top of my head thoughts. You have fire when there is oxygen. So when an explosion happens in space, will be pretty short-lived assuming it's fueled by air rushing out of the spaceship. Assuming Helium 3 has some properties like ordinary helium, helium is normally inflammable so it would not explode like hydrogen, but if the temperatures and pressure gets hot enough it will start a fusion process. Only it will be much cooler than if hydrogen fuses. Instead of blue or yellow, the flames would probably be red. Someone who is a physicist or astronomer could probably confirm my theory, but it's worth considering.

Magnetic crunch

Where the magnetic force crunches the craft inward like car crunch press after it is hit with laser weapon and makes a bloody mess. Some crafts make it into orbit before crunch then the steel chunk falls to earth, creates a deep hole in the ground and earth waves travel outwards when it lands. One lands just out of Toronto and the wave runs through the city. Buildings collide and the CN TOWER brakes,,falls into the City( shot from outside goes through the window in tower..shows people sliding inside the tower,and the camera travels out side to see the tower fall into the city..in one shot) pulling the elevators up the shaft. Everyone escape when the deck around the tower hit buildings on both side of Young Street and slows it down until it stops just above the street and one guy falls to the ground, unharmed and the tip of the tower brakes off and spears a car on the ground.

"I just like it when stuff blows up"

Having had a look through the other suggestions people have made, i don't know if i can really be of any assistance! However, i do know of a couple of explosion effects that could be suggested as the explosion of Helium - 3 (depite the fact that i know nothing of Chemistry and have absolutely no knowledge of the science behind it! :P) and i would just like to add that i use film examples not because i encourage plaguerism but because they best describe the types of explosions i was thinking of!

1. Star Wars - Attack of the Clones: The Seismic Charge

I'm not suggesting you plaguerise George Lucas' sci-fi epic!!! i just think that this explosion type, in form and colouring could fit the bill for what you are suggesting! (see image #3)

2.The Hindenburg -

I have sufficient knowledge to know that helium itself is inflammable and would not explode like Hydrogen gas does. But i thought the way in which the fire moves and spreads (much like a solar flare) could be used to simulate an explosion and i think the way the explosion causes the airship to sink, as though in water, could be used as well! (image #1)

3. Titan A.E - Earth Destruction -

IF you have seen the film Titan A.E the way in which the earth is destroyed, exploding outwards with multiple fragments flying in all directions could be used in a ship explosion. (image #2)

Catastrophic Containment Failure.

FAST FORWARD TO 3:12

As the core containment field fails, light pierces through the bullet-hole riddled hull. The core-plasma, formerly contained by magnetic fields, vents into the interior compartments, and the crew is vaporized.
The hull screeches under the pressure, and with a metal-rending
explosion the 'Haunebu' is torn asunder.

All that is left now is a quickly dispersing glowing plasma cloud,
and a couple of after-shocks as the ammunition explodes.
This could happen in a daisy-chain fashion, or maybe the one
or other round is launched to careen off neighboring ships.
Some internal fragments might be molten, and will be able to
pierce armor like an EFP.
http://en.wikipedia.org/wiki/Explosively_formed_penetrator

Does this sound like it could be fun, or what?

Another similar video:

Explosions, Fire in Space....YEAH

Ok so you have space flyers scrambling, setting out all sorts of munitions. Why not use the space debris as reflectors. As space junk is floating by causing all sorts of manuevers for the pilots have a weapon that can bounce once off of the debris hitting a target then exploding.

Example:
Nazi craft is targeting enemy craft there is pieces of a recently launched rocket nearby A canister is launched by the Nazi craft that deflects off of the space junk at a trajectory that hits it's target. causing the enemy craft to impolde upon itself.

Also looking at the Norway Sky spiral might give some ideas as to using advanced technology, and would give off shock effects to the viewer. Like the battle in space is causing all this phenomina on Earth.

Example: A hit craft goes into a spin losing a spiral like gas into space then finally imploding. From Earth view it looks like the Norway Spiral.

Also another type of explosion you could use is transient black hole effect.

Example: A canister containing dark matter is shot with armor piercing capability. It hits and imbeds itself into a ship, a timer goes off and the dark matter chamber breaks disolving the ship into nothing causing an area to avoid by future space fights.

Plasma

So, I suppose they use Helium-3 in a fusion reactor. That's what it may look like during normal operation:

When it escapes, I can imagine it to look like that, but 1000,000x more violent:

More plasma:

conventional roceteering damage

I am assuming that the battle is fought near earth and some of the damaged ships might enter earths atmosphere with bad results.

100 million dollars of damage

Major Malfunction

Re entry demolition

Columbia

Mir

and a little something for the genre

Mini star

Nazi ships could use non-fictinal Helium-3 as fuel. Non-fictinal Helium-3 is rare on Earth but it's thought to be greater in abundance on the Moon. Moon Nazis could

process moon regolith to make Helium-3. Helium-3 can be used as fuel on fusion reactor. Only down side is that fusin Helium-3 with itself or even with Deuterium requires very high temperatures.

Moon Nazis overcame this problem, but those shorcuts made inherently safe fusion reactor prone to hyper-accelerated chain reaction with catastrophic consequences. In normal operation reactor is perfectly safe, but with sufficient combat damage reactor could accelerate out of control. This would result reactor to become kind of a mini star.

It would melt the ship to form "star's" outer somewhat cooler surface:
Resuling fire ball like these but in smaller scale:

When "star" has consumed it's fuel and fusion reaction is dying, it first lose it's outer surface like giant solar flares:

Then collapsing into intsel and finally exploding:

After explosion all that remains is some gasses in near ships posiotion.
Result:

Underwater

Check out how it pulsates (especially at sec 23). Almost like a beating heart. The more organic it looks, the more violent it will appear in my opinion:
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