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I'd recommend trialling the software, both commercial and freeware. Even commercial software has its strengths and weaknesses. I often find I'm diving in and out of different applications as one will perform a specific task with more accuracy or provide the user with valuable feedback so you know what's going on. Which leads me to a key point, whatever software tool you choose, stick with it. Learn it inside out and know what it does to the data. I've seen people flame software on other forums because it didn't do the right job. 9/10 times, its the user's inexperience. Some tools are not as intuitive as others and take a while to pick up. It is all a part of the imaging learning curve. When trialling the software, don't solely focus on the stacking, but review the tools overall features to justify whether it worth.
At the opposite end of the scale, the only freeware software tool I've used is CCDSharp with is for deconvolution, not stacking. I presently utilise CCDStack and MaximDL for the grunt work such as stacking. I'm happy to discuss both of these in further depth.
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