Ordering weapons is key to great ship design. As others have pointed out below already and as the faq illustrates.
Here is another example.
Temporal Weapons
You want to put the shield/armor skipping first.
In this way they fire first and you have a chance of hitting any shield generators and taking them down.
Next the Time Distortion Bursts for the 4x to shields damage. If you don't take the shields down with the skippers the distortion burst can weaken or take em out.
Next you have the damage weapons of your choice be it PPB or APB or DUC or some nice Tachyon cannons. With shields weakened as much as possible already it is time to take em down.
Of course other specialty weapons such as tractors and repulsors and wormhole beams all have their own places as well. Depending on your strategy.
Already mentioned was the ripper combo. But there are others.
Think about it and see which ones you can come up with and you might just find yourself in command of a near invincible fleet.