Registax and Autostakkert are mainly used for stacking planetary, Lunar, or Solar images. Once you've stacked in these programs you would do some final colour tweaks etc. in Photoshop or Paint Shop Pro. For this kind of work Paint Shop Pro will do the job, but if you're not going to use Photoshop you may as well pay nothing and use
Gimp.
For deep sky imaging you'd use different software to stack. The most popular free one is
DeepSkyStacker. After you've stacked you will want to do things to your image to make it look better and make it look the way you want. You can do these things in Photoshop/PSP/Gimp or you can use a more specialised astro specific program, like
Startools, Pixinsight, and many others.
Personally I stack and process my images in Pixinsight and do final colour tweaking in Lightroom, or sometimes Photoshop.