Ahaha,  I like it.  I think the lighging could use more work, to help it blend more, but I couldnt tell you what to do to make it better. how did you do this though? alpha channel? render with a green background? how about the complex motion tracking to get thigns to line up?

 Of course that's very welcome!  Well done there too.  I think the second ships probably fit in best, though I do agree that some of it could use a bit of work.  It does look semi-realistic though.  The explosions and smoke I think needed the most work.  They didn't look realistic at all.  The sound effects were okay, and I loved the focusing, it helped add to the realism.

I would be interested in how you went about doing this as well.

 Tutorial! tutorial!

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Alright now for some crits haha, I think the ships didnt really fit in too well, because of their sense of scale and distance. One thing that could improve it a lot is to give it some distance fog, ships that far dont have saturations like this, but because of the atmosphere/smog it would be a bit more gray/blue, you should be able to put some sort of distance color/contrast filter over it. 

As for the lighting, I think the best way to go is really to look at the buildings & objects in your clip, then try to simulate that lighting as best as possible. You got the direction of the sun correct, but it could use a bit more yellow. Also the shadow side of the ships could have used some very slight blue color.
You could even make a shadow of the ships falling on the buildings and stuff, but thats a bit more work ;)

One more thing; the ships came a bit too close too fast, before they shot at the camera.

Good work though! and good luck on either improving this video or with the next one ;)

Thanks for the comments, guys; they are very helpful!

As to how it was done, it's pretty straightforward.  Export your image sequence and the alpha channel from Anim8or, then import it into After Effects and run the Motion Tracking feature.  Motion Tracking basically takes your live action video and tracks the rotation and position frame-by-frame using keyframes.  You can then apply these keyframes to your Animation track and voila!  It works pretty well although sometimes tweaking is necessary.

As for this video, it sounds like lighting is a big issue.  I did make a bit of an effort to match the lighting of the scene in Anim8or by using a reference frame as a backround in my Anim8or scene, but it looks like I could use some more practice .

In terms of filtering, I did do a little bit of that already, simonjaap.  Initially the Star Destroyers looked a lot sharper than the live-action video so I applied a Lense Blur to try and make it blend better.  I didn't try any atmosphere filters in this video though, but that's definitely a good idea.

Again, thanks for the comments.  I think I might try some more of this sort of thing in the future.