Fretslayer

Thinking about what you are going after I would think that Flash would work perfectly for you.

Have you ever messed with it before?

You can make the wepon fire in Photoshop (save it as a gif) then import it into Flash (the background will be transparent) and when the ship fires it toward you, you use the 'Tween' feature and then just scale the size of the plasma burst to something larger and it'll appear to come closer.

Also you'll be able to take a still shot of the Starships (from a few different angles) and import them into it as well.

Plus Flash animations take up very little bandwidth (when you want them to) and most people can already view the files.

Another thing is that you work in layers just like Photoshop.

If you're going for the TV TOS look and things like specularity and bump mapping aren't that important then Flash might be good tool to look into.