I just set up Skype for Linux here on Hal's Formerly Evil Twin.*
I downloaded the deb file, did the sudo dpkg -i thing, plugged in a Logitech USB headset, and fired up Skype. Voila! I logged in easily, I set up Skype to use the headset to talk and listen, and made the test call, which worked fine — except that it about blasted out my ear.
Since I didn't change the default sound system, which is still alsa, none of the standard volume controls would turn down the sound. I looked around the web, and finally found the answer here. You have to explicitly tell your system to turn down the volume on the USB device. For my system it's dsp1, but your mileage may vary. To get volume control for dsp1, open up a terminal window, and run
alsamixer -c 1
This will bring up an interface where you can adjust the volume — with the arrow keys, not the mouse, it's a text window after all.
It apparently works, though I'll have to wait for my ears to stop ringing to be absolutely sure.
*Do not give me a hard time about using unfree software. This is a work related project, and I have to make compromises if I want to keep getting a paycheck.