To take the pictures, I use the EOS Utility -- in the Remote Shooting mode, there's a timer option where I can set the number of shots and it'll automatically keep shooting. For deep space objects with my telescope, I use Nebulosity (which provides different/more features). I know some people use a remote control timer like [ame="http://www.amazon.com/Canon-TC80N3-Remote-Control-Cameras/dp/B00009XVA3"]this[/ame]. The advantage of using a software control (like EOS Utility or Nebulosity) is that you can see the results as they're being captured and can correct anything if necessary + it records directly to the computer so no danger of filling up the CF card. The downside is that you have to have the camera connected to a computer (which may not be feasible far out in the field). With the timer remote control, it's just the camera + remote (not to mention that Nebulosity does not support many DSLRs since it was designed mainly for CCD imaging).
Once the images are captured, for star trails I stack using Image Stacker. Very simple and easy to use. For stacking where I want the stars to be added without any trails (like this, which needs each frame to be rotated/translated), I use DeepSkyStacker.
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