No they cannot under normal circumstances. They would have to installed some sort of remote control device or trojan on the computer to see all the programs installed. They could guess at some of the programs by observing data traffic to and from the computer because each program that accesses the internet has it's own identifiable port(s) or window(s) to do so but that would take a lot of resources that would not normally be used except under extreme circumstances.

In any case if the ISP installed anything like that on his computer it would be illegal (and unlikely since it would open them to huge lawsuits) and interfering with his Skype acc't would not only also be illegal but they'd need Skype to agree to conspire to do so and that would be an even bigger legal problem.. and I'm talking multimillion dollar class actions.

Is it possible that they just guessed at some of the more common programs that everyone has installed? But even so why would they do that? Doesn't make a whole lot of sense.