My newest proposal is a new, ultimate ship killer missile.  The emphasis on this mega-bomb is the engine core of capital warships.  Anything less than atleast a destroyer or cruiser is gross overkill.

The core of the bomb is a small atomic bomb, a rarely used weapon since many of the shields used today counter both the weapon's yield and radiation.  This should not be confused with the hydrogen bomb or the proton torpedo.  The hydrogen bomb is a controlled fusion/fission detonation, and the proton torpedo is a small nuclear bomb that sacrifices yield for power.

The atomic bomb has one feature that makes it suitable for a ship-killer: an EMP.  An Electromagnetic Pulse will overload circuits and cause them to reset.  While this may not seem to be dangerous in and of itself, but I'll come back to this later.

It is well known that the cloaking technology renders both the ship being cloaked invisible to sensors, but also renders it's own sensors useless.  The importance of this is that it is possible for ships to move in and out of the cloaking area.  This is useful for a delivery system.

A cloaked ship, mounting a sensor pod (such as on the Recon X-Wing), could deploy a sensor pod outside of the cloaking area long enough to move into a crowded shipyard without hitting another vessel.  From there, the sensor pod is lowered and information is gathered for a target.

It is common for warships to keep their shields down when not in combat.  The reasoning behind this is because it is easier to send communications when the shields are down, especially for long range communications with command.  With no shields, that means that the only shields around the engine core are the magnetic containment bubbles.

These are not the same as standard magnetic containment fields in that the standard fuels of capital ships are highly magnetic.  The magnetic bubbles keep the fuel from touching the containers they are housed in.

The atomic bomb, when launched, will have a hardened cone over the front of the bomb, and a slam engine on the back.  Because charges must go off to start the fission process, the slam engine won't affect the bomb's effectiveness.

Once the bomb is launched, and leaves the cloaking field, it will be detected, but moving so fast it will be impossible to stop.  The hardened cone will protect it long enough to get inside the engine nozzle, and when it detonates, the magnetic containment bubbles will be directly affected, so that if not reset by the EMP, then destroyed by the explosion.

The amount of fuel inside the ship, if not full from a recent refueling, will atleast have 25%.  This is the standard marker to allow vessels to make it to other stations incase the station in question is in danger.  That amount of fuel will detonate with such force that it will utterly destroy the ship.

Since the cloaked ship will be at the launch point, it will naturally have to retreat, but with such confusion and a head start over the enemies, there is only a small chance that the ship will not be able to escape.

Diagrams:
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^                    ^                ^
|                    |                  |
|                    |                  [Reinforced Cone]
|                    [Warhead]
[Slam Engine]
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FM/CRW Linda_Irris/Sting6 (2-2)/Wing2/ISD-II Devastator/Offensive/VEN/VE

This reminds me of an episode of "Stargate: Atlantis" where the good guys send in a nuclear device to a hive ship and detonate it.

Once again, it's a great idea in my opinion, but how about without using a cloaked ship, have the atomic bomb onboard a Star Destroyer where it would replace a few other launchers on all sides. Then if an enemy ship comes too close, (example in Episode III where two enemy ships battle it out in the opening battle), the Star Destroyer could launch this weapon straight at the enemy ship's targeted core.
 
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Revenge is what holds this galaxy together. Without it, the universe would be a boring place.

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Senior Chief Petty Officer and Reporter Jack Nebulax (*Formerly and No-Longer a ComNet Spammer*), Imperial Navy and VE Today Staff, Vast Empire.
XO/FL/SCPO Jack Nebulax/Nazgul 5 (2-1)/Wing 1/mSSD Atrus/Defensive Fleet/VEN/VE (=A=) (=*SA*=) [SV] [VC:S]
Rep|Int/Rep Jack Nebulax/Rep: 4/Reporters-Interviewers/VE/VET
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Admiral Jack Nebulax, third-in-command of the Auroran Defense Fleet (ADF) and leader of Nemesis Wing (Wing I)

Well, then, I guess I thought of another way that this weapon could be delivered. I just thought the double-blindedness could actually screw up the deliverment of the weapon.
 
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Revenge is what holds this galaxy together. Without it, the universe would be a boring place.

------------------------------------------------------------
Senior Chief Petty Officer and Reporter Jack Nebulax (*Formerly and No-Longer a ComNet Spammer*), Imperial Navy and VE Today Staff, Vast Empire.
XO/FL/SCPO Jack Nebulax/Nazgul 5 (2-1)/Wing 1/mSSD Atrus/Defensive Fleet/VEN/VE (=A=) (=*SA*=) [SV] [VC:S]
Rep|Int/Rep Jack Nebulax/Rep: 4/Reporters-Interviewers/VE/VET
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Admiral Jack Nebulax, third-in-command of the Auroran Defense Fleet (ADF) and leader of Nemesis Wing (Wing I)

well it's mostly a ship killer, and if there are other uses that's cool, I just thought I'd throw this idea out there.
 
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FM/CRW Linda_Irris/Sting6 (2-2)/Wing2/ISD-II Devastator/Offensive/VEN/VE

There's a problem with that: sheilds.  a ship could also target an incoming commando team and stop them.  I imagine in a big battle they could do it, but with so much firepower being exchanged, that's alot of risk to just plant a bomb.  Also, the soldiers would be sitting ducks while protecting the bomb.

Also, there's something that very few know about.  It's called the Bikini Atole Nuclear Tests.  They tried detonating a nuclear bomb near a battleship.  The ship only suffered minor damage.  That means that with a modern warship, with thick bulkheads, magnetic containment fields, and other defences, there is little that a single bomb on it's own can do (that's why when Rouge Squadron fired proton torpedoes at the Lysankya [I spell bad], the ship mearly broke off at the nose instead of blowing up.)

So that means that while it sounds good in theory, unless you hit the engine, it doesn't work.  And the ability of a single commando squad making it all the way to the engines, arming the bomb, and then escaping, doesn't equal the payoff.  Again, great idea, just not possible.
 
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FM/CRW Linda_Irris/Sting6 (2-2)/Wing2/ISD-II Devastator/Offensive/VEN/VE

Believe it or not, that was the first Stargate: Atlantis episode I ever saw. Now I watch it whenever it's on.

Back on-topic, how about my idea? With launch tubes on an ISD being replaced by tubes for this? Have some placed at the front, the back, and both sides. That way, whenever an enemy ship comes at the ISD, it can just launch two atomic bomb toward its engines. One to knock out the shields, another to detonate at the engine housing.
 
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Revenge is what holds this galaxy together. Without it, the universe would be a boring place.

------------------------------------------------------------
Senior Chief Petty Officer and Reporter Jack Nebulax (*Formerly and No-Longer a ComNet Spammer*), Imperial Navy and VE Today Staff, Vast Empire.
XO/FL/SCPO Jack Nebulax/Nazgul 5 (2-1)/Wing 1/mSSD Atrus/Defensive Fleet/VEN/VE (=A=) (=*SA*=) [SV] [VC:S]
Rep|Int/Rep Jack Nebulax/Rep: 4/Reporters-Interviewers/VE/VET
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Admiral Jack Nebulax, third-in-command of the Auroran Defense Fleet (ADF) and leader of Nemesis Wing (Wing I)

Well, I didn't mean to take out all of the proton torpedo launchers onboard a ISD but just to replace a few. Also, an ISD carries small ion cannons on the sides, so we use that to puncture a small hole near the engines and then launch a bomb through the opening into the main engines.

We should create a new division called the Research Division. I've seen many Star Wars clubs have such a division. That way, we could test new weapons and crafts and improve the older ones. How about it?
 
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Revenge is what holds this galaxy together. Without it, the universe would be a boring place.

------------------------------------------------------------
Senior Chief Petty Officer and Reporter Jack Nebulax (*Formerly and No-Longer a ComNet Spammer*), Imperial Navy and VE Today Staff, Vast Empire.
XO/FL/SCPO Jack Nebulax/Nazgul 5 (2-1)/Wing 1/mSSD Atrus/Defensive Fleet/VEN/VE (=A=) (=*SA*=) [SV] [VC:S]
Rep|Int/Rep Jack Nebulax/Rep: 4/Reporters-Interviewers/VE/VET
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Admiral Jack Nebulax, third-in-command of the Auroran Defense Fleet (ADF) and leader of Nemesis Wing (Wing I)