We have a heavy Ajax dependent application. What are the good ways of making it sure that the request to server side scripts are not coming through standalone programs and are through an actual user sitting on a browser
There aren't any really.
Any request sent through a browser can be faked up by standalone programs.
At the end of the day does it really matter? If you're worried then make sure requests are authenticated and authorised and your authentication process is good (remember Ajax sends browser cookies - so your "normal" authentication will work just fine). Just remember that, of course, standalone programs can authenticate too.
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