After playing with the defaults, I changed the settings to make my Skype and headphones jack work.
Below are the settings that work fine for a Thinkpad T62
Below are the settings that work fine for a Thinkpad T61
Below are the settings that work fine for a Thinkpad T60
Below are the settings that work fine for a Thinkpad R50
Your millage may vary, but I would start to set everything to "Pulse". And if in case Skype does not work, change "Input Source" on Volume Control and pick the right Mic, if that does not work the next step would be to change Skype "sound in" setting to the first ALSA device on the list, as the example on T60.
Some Folks reported huge latency with pulse audio on skype calls, here is a config for skype using only ALSA on a T61:, this should fix the latency problem. You might need to execute "killall pulseaudio" to stop pulseaudio.
Thanks to: Marcin Bogdanski for the T61 config
