I dont think that skype causes to much of a drain, but I have only used it a few times. I was using it in germany to call home for the cost of internet use wherever I could get wireless access.
The poor wireless connection was more to blame for the battery usage. It is good if you know you will have a wireless connection, such as a hotel or internet cafe, but overall it is a crapshoot.
Edit- Another item to consider is that typical bluetooth headsets will not work with the 3rd gen touch. Maybe the new ones, but I cant say for sure on those/ The apple support forums could provide an answer pretty quick. I was using the headphones with mic that came with my moms iphone.