Depends on the directory itself.
By default, Java will not install to C:\Java, and if it was not installed there (and a good indicator that java.exe or javac.exe are not available in ./bin there, or check the system path to see if its registered), then you would be fine to delete it.
java.exe will by default install on windows to C:\Program Files\Java\jre#\bin, where # is the version number of java. You definitely don't want to delete this, which is why you need to check if it was installed to C:\JAVA\jre#\bin, which would make that the valid installation path.
As of PHP 5.5, the MySQL library has been officially deprecated. It is recommended to move to either MySQLi or PDO libraries for your mysql connectivity. See here for help choosing which interface you prefer: http://php.net/manual/en/mysqlinfo.api.choosing.php