I cannot use the GPL licence on something like a G.729 implementation, because it is patented. Right?

This appears to be the case, from reading sections 7 and 8 of the GPL version 2. Section 8 allows for geographically limited distribution. However, most of the patents relevant to VoIP have been granted in most places, so you would be geographically limited to those places with too small a market to encourage the patent holders to file their patents there. That seems pretty close to no GPL implementation being practical. There may be other signal processing functions where the only relevant patents cover computational methods. Right now, these patents will only exist in the United States. Here, a fast GPL version distributed only outside the United States, and a slower GPL version distributed within the United States may be possible.