Best bet would be add all of your target folder files into a dictionary. This way you can just use "Exists" to search for it in the dictionary.
Set fso=CreateObject("Scripting.FileSystemObject")
Set filesDic = CreateObject("Scripting.Dictionary")
Set targetfldr=fso.getFolder(targetpath)
'add destination files into dictionary
For Each file in targetfldr.files
filesDic.Add file.name, file.name
Next
This way all you need to do is check the new filename against the dictionary
filesDic.Exists(file.name)
This will just return a true / false
Here is a bit more information about the dictionary http://www.devguru.com/technologies/vbscript/13992