Cloaking effects are fairly easy to concoct in AE if you have the right source material. The trick is to render out separate layers for the different CG elements. The simplest effect being a ship clocking in open space. For that you only need to layers, the stars and the ship. Now, most 3d programs allow you to render to some form of image that includes an alpha channel, make sure you use it so you can use the alpha as a mask for the ship.
One you get your layers in AE, apply an effect like ripple and maybe layer on some keyed color effect or a blur at the same time and then over the course of 50 frames or so, dissolve out the effected layer. Granted I'm not trying to write a tutorial but rather give an overall idea of the process. The key elements are separate 3d layers and key-framed AfterEffects filters in the in it's just turning down the opacity on the ship layer from 100% to 0.
As for phasers and other such I tend to use particle effects in Maya to create the beams and then comp them in in AE adding blur and glow to make the finished layer. Again the phaser beams on ships exist as a separate layer for maximum controlability outside of the 3d app.
