NMAP
How to change user agent
You can find the default value in /usr/share/nmap/nselib/http.lua (At the beginning of the file, a couple of lines after the comments)
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local USER_AGENT = stdnse.get_script_args('http.useragent') or "Mozilla/5.0 (compatible; Nmap Scripting Engine; http://nmap.org/book/nse.html)"
You can change the value with this line
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local USER_AGENT = stdnse.get_script_args('http.useragent') or "Mozilla/5.0 (compatible; MSIE 9.0; Windows NT 6.1; WOW64; Trident/5.0)"
You can set it to whatever you like, stealth is key, change it periodically etc.