I have been using skype on a 3GS for over a year with absolutely no problems whatsoever except the occasional hang until last week since when attempting to call any phone number or skype account the sound does not function. I haven't changed any settings and I am running version 3.01(250). The phone is working absolutely perfectly otherwise.
Please try to upgrade to the version 3.5 from the App Store. If the problem persists, please reply back.