...I never can decide between these two. I'm always going back to the code and switching between.
When you're coding - let's say a Login class - from an (extended) HttpServlet, which sports both ServletException and IOException, and you just want to throw further your exception (e.g. NoSuchAlgorithmException, NamingException) to see it in a page of your application later, which one do you throw it through: ServletException or IOException?
P.S.: I don't try to catch every possible NoSuchAlgorithmException, NamingException, etc. because I can miss a real cause that I haven't seen before and treat it the wrong way or inform the wrong thing to the user.
IOException has its own meaning. An IOException should be only thrown when there as an issue in IO operations e.g. reading/writing data from file or URL. If I have to make choice between the two, I will choose ServletExcetion.
But if there is a room to define better exception handling then I would like to create my own custom exception class e.g. MySystemException extending RuntimeException and wrap the relevant exceptions as MySystemException and throw it.