SSH still works on 4.1. I have a 3GS as well. Use another SSH program and it'll solve your problems. Also, if you are connecting via USB rather than SSH, then install afc2add on your iPhone which will enable USB connections.
Not sure if it works with 4.1, but for me iPhone Folders broke when upgrading to iTunes 10. The fix was to find the iTunesMobileDevice.dll file and replace it with the one from iTunes 9. Not at my comp right now so I can't upload mine at the moment, but I can do that later this evening if you'd like.