Took me a while, but after more careful digging, I've figured out what is happening. Last.fm is indeed lying. They are not listening to your media players. They are listening to your sound card output. Disabling sounds in Skype will disable every Skype event log except for two - updates to mood/music playing, and any time you make a skype call. Those to events trigger Last.fm logging. In the log, there's no real identifying information. What can be gleaned, though, is how long you made that call.
"If you choose to download the Last.fm software, it will monitor all the music you listen to on your computer (even if you are not online). It will then send this information to Last.fm via Audioscrobbler. This information will then be integrated into Last.fm to enhance the depth of your record collection and the accuracy of your profile.
The Last.fm software cannot and will not collect and transfer any other information from your computer other than as described above."
That is a flat-out LIE. And you're not even told about the integration with Skype when you install Last.fm's Audioscrobbler. You have to find out yourself by looking through log files, or go back to an obscure 2006 Skype Blog post.