These are all pretty good suggestions, most of which we're aware of and many of which aren't, unfortunately, as easy to implement as you might think. But we do hope to make all of this kind of stuff easier, I can say that. In the meantime here are some suggested workarounds/workflows that may help.
For comparing images/crops/etc.:
First turn on automatic output of renders in Preferences -> File Saving. I recommend setting output format to TIFF 8-bit ZIP as TIF is widely supported and the ZIP compression will save space. These images will also be saved whether a render finishes or not, so that's useful, you can abort and compare even if you didn't want to wait for it to finish.
Then, get a good, fast image viewer that allows you to quickly switch between two or more images. I use XnView and Faststone, both are excellent and free.
http://www.xnview.com/ and
http://www.faststone.org/Finally, when you open Terragen for the first time (and each time you create or open a new project, since the folder changes at this point), go to File -> Explore Automatic Render Output Files. As soon as you do your first render, a new folder will appear in there, go into that and you can open your automatic image output(s). Images will continue to be saved there automatically each time you render (again, whether you let it finish or not). These can be easily compared with the image viewers above. I just mouse wheel scroll between different crops, for example. Also takes care of the zoom issue as you can zoom all you want, quickly and easily, and even preserve zoom levels between different images you're viewing.
For the Population on/off issue:
Put all your populations in a Group, then just turn the group on and off.
For the atmosphere rendering issue:
This is not a total solution but IF you use Raytrace Atmosphere, then the Antialiasing value becomes a quick multiplier for quality. It's non-ideal because it also affects quality of objects, etc. but it could be a useful idea to consider.
- Oshyan