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Is it on topic to ask questions of the form "What program does allow me to do X"? Or more generally, is it on topic to ask questions about recommendations for certain programs? I fear that these questions may be suited better for superuser.com...
Yes, this is on-topic. We already have many questions like this.
Yes, there is some overlap with SuperUser, which is unfortunate. But in general here you are asking *nix experts for advice on apps for your *nix system, which seems appropriate.
As long as you don't ask something like "what is the best web browser to use on linux and windows?" you're probably fine.