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To be direct, I am very surprised this question
seems to be considered accpetable (being open since a day, with only two votes, one by me, to close so far).
As I pointed out in a comment, the way it is phrased would even admit anwsers like 'a webbrowser'.
Now, I am willing to admit that this is a bit of a silly overinterpretation, and OP argues that the examples given should make the intent clear. However, in my opinion, this is not as much of an overinterpretation. Version controls systems are mentioned and an anwer is some syncronisation tool. IMO these are essentially as standard programs, though perhaps less wide spread, as a text editor or a browser.
Furthermore, the notion of software/programm underlying this question is very broad (including such things as OEIS, which IMO is mainly a collection of data/a database which most people I guess access via some web-frontend).
So is any useful mathdatabase ontopic or is the criterion that it does have a nice frontend?
Say, the Cremona's tables of EC are useful, there are handy ways to access them, so if OEIS is ontopic I guess this would be too.
Or, LaTeX is mentioned as example; I do not want to do some hairsplitting whether LaTeX is a programm, but what I find starnge is that then 'beamer' (a documentclass for LaTeX) is mentioned in addition. So, amsart is also useful, I guess this would count as silly answer; but I guess if I named some documentclasses for creating posters this might count.
Should all this be collected in this one question?
In particular, some things are really duplications of existing questions.
Which I pointed out, yet OP did not follow up.
Well, in brief, to me this question is an instant close; 'tools' question are always a bit difficult, but if it is as unfocused as this one...
Apparently it is not. What am I missing?
It now has four votes to close. One of the first two was from me and I agree with quid's reasoning. I notice that rsync has been mentioned .. which underlines the argument in my view.