I'm planning to make a search engine, so I've downloaded this script. It works well, but I have to add a list of websites manually in a php file for the search engine to index. Is there any kind of database/file which lists a real lot of sites?
Also as of last year there were only 70 million sites which Yahoo indexed.
So you get all the domains and then fetch their Alexa rankings and start indexing in ascending order of rankings.
There are over 600M websites in the world, and that number is probably going up 1000s a day. I don't mean to be an ass, but a $14 script and any webserver you come up with isn't going to be able to be a remotely fast or effective search engine.
Use something like Google Custom Search to setup a a Google frontend just for your websites, or if you actually wanted to rival Google just give up now.