After trying lot of free tools to backup my MacBook Pro settings, selected applications, user and system settings; nothing found interesting. But today I found iBackup as the best one so far whatever the tools I tried. Which is a nice free GUI tool, offers to backup selected user and system settings along with the applications and utilities; which is what is needed when I needed restore back the OS because I do not care about reinstalling the Mac OS X back, but more concerned about the settings and core files.
It took me about 20 minutes to copy all files (~1.4GB) to my other backup Windows drive (smb mounted). So, even if I break the OS, I can get my settings back by restoring the files using iBackup. Now, I can schedule the backup process for every week.