My free AVG software detected the js/download agent and i was wondering what kind of damage it could do. I read that if i cleaned up my java files it might clean the virus. I did this and it seemed to have worked, is the virus still there? is there anyway to make sure?

JS (JavaScript) have nothing to do with Java (apart of similar names).
JS is mostly a part of web sites, and JS is used for making interactive content on web sites.
On other side, JS can be used to do actions like downloading malware to your PC.
A downloader + agent means it will download and run some executable file on your PC.
It does not do any damage by its self (can't delete files or something like that), but the file it downloads can do every kind of damage if it is a malware.

So, if your AVG did detected this downloader while you visited some web site - it means that the downloader did not have had a chance to download and run malware.
But, if this downloader was detected later, at "on demand" scanning of your HDDs, it means that the downloader already served its purpose, and your PC may be already infected.