If you're running a serving script, it could simply be that it's indexing your files. If you have a lot of files, this can take time.
Otherwise, good scanners for trojans are:
Ad-Aware
Spybot Search & Destroy
Good browser hijacker scanner (obviously not what you need here):
Hijackthis
Just be careful what you remove when using thse programs, as they can bring up legitimate files. Usually, you can tell what's legitimate just by the extension or extra information given about the file.