“System”, “software”, “application” or “tool” – which to use in my paper? I am in the field of computer science, I developed some software to solve some problems and would like to write some papers about them. But I don’t know what to call the software in each of my works.

For example I developed software to extract structured data from web pages, (I called it system). In another project I developed software for foreign language learning (I called it software tool, however I may rather to call it system again).

In general, what is the difference between software and system? 
When I should use the terms application or tool?
Software, system, framework, application, and tool, along with several other words are often used to describe computer programs that accomplish a task. Application tends to be used when it is a standalone program that accomplishes the task, whereas library is more used when the code in question is intended to be used directly by other programs through an API of some sort. Frameworks often incorporate multiple libraries and/or applications to accomplish a broader set of goals. Tools tend to be smaller programs that are sharply focused on particular tasks, though through scope creep they often lose this focus over time. System frequently implies a much larger whole and is often used to speak of hardware/software systems (like a whole computer) as well as software alone. 

These words have specific meaning in some contexts, but are often used somewhat interchangeably as well. It would be best to have a native English speaker in your field look over a few sentences that use your preferred words to make sure that they are consistent with your field's use of the terms. You may also compare to similar works, especially those you reference and those in journals or conferences where you'd like to publish, to get a feel for what the norms are.