Question: Because of some reason my site stopped working. After that I have uploaded the backup which I had created earlier.

I am getting a "404 Not Found Error The resource requested could not be found on this server!"
getting this on every page except `index.php` and also not able to login into the admin panel.

I already cleared the cache memory and set the `is_active` option to 1 in `core_website`, `core_store` and `core_storegroup` tables in phpMyAdmin still getting an error... I've tried so many links to solve this issue but the problem didn't resolved till yet.

Answer: 
It sounds like a behavior which can happen if you do not have the ".htaccess" file by Magento or if the ".htaccess" file is messed up. 

Please try adding or replacing the current file with the default ".htaccess" file from Magento.
the solution for 404 errors on magento 1.9 was to 1-reindex data and 2-flush cache storage