For me it depends on what I'm trying to image.
If I've used my camera to image DSO's or clusters than I use Deep Sky Stacker to stack my images. It is easy to use and does a good result of shifting, rotating and deciding the best images to use.
If I've used my QHY5 to take avi's of the Moon or planets then I use Registax5 (or 6) to stack. I especially like the wavelet processing within Registax - it really helps bring out definition in these bigger objects.
I then use Photoshop or Startools to enhance, correct and tart-up my images.
I hope this helps...
Mario
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