Well, I would suggest again that you simply look at what Google has indexed and you can safely assume that the others have NOT been indexed..
backlinkwatch looks for links pointing to the URL inputted.. so this is NOT what you want..
Again, If I understand you correct, you are have a bunch of webpages which I am assuming are from the same domain that you want to know if are currently indexed or not..
Well, you have one database that has URLs, and Google webmaster tool will provide you with the URLs that are already indexed. simple reduce the ones which are indexed to the original database..
The other way is to simply scrape URLs from a search using advanced parameter like
"site:URL" which will provide you with all the URLs that google has indexed on that site
(not very reliable though)
now if all these URLs are from different domains, then you have a problem on your hands..
you will need to create a custom tool for that..