I need to transfer binary files from my pc/mac to my app. I want to allow my users to upload sound files. Am i going to have to run a web server that the user can connect to
Do you need to transfer the files program-atically or through a GUI? If you can use a GUI, enable file sharing, and use iTunes>IPod>Apps>File sharing to drag and drop / load files to and from your application's Documents folder.
If you need to do it programatically, here is a technical note describing different strategies to do so: http://developer.apple.com/library/ios/#technotes/tn2152/_index.html