I recently asked people on Mastodon about the ham radio logging software they use on GNU/Linux. Here is the list that came up.

PyQSO, klog and CQRLog are in Debian archives, which means, it is easy to install them (along with their dependencies). CQRLog and YFKLog has LoTW integration. It is not hard to do signing and uploading using the separate tqsl program. But these logging programs automate them. Of all the programs, PyQSO seem like the easiest to use. All the database is contained in one sqlite file.

I also found a couple of other programs worth mentioning:

I am currently starting to use cqrlog, but I am going to try PyQSO and see if that works out fine for me.

edit: 10/April/2020 - I setup N1MM and it has been nice to use. I will have to stick to it as long as I don't find an alternative to PowerSDR that works as well on GNU/Linux.