What to do when the tools I am supposed to compare my work with are no longer maintained and functional?
I see a few ways on handling that:


write to the editor that the tools are unavailable and let him decide what to do with your paper.
add a passage in your comparison section stating that due to unavailability of those tools the comparison was not carried out.
ok, the authors don't reply. But if the reviewers want the comparison that probably means that at least someone is still using the tools in question. Maybe you can get in touch with some other laboratory that has the executables and run the necessary tests on-site there?