Your media player is spying on you too. In the case of windows media player, when you are playing an mp3, the get album art (cddb) feature sends your ip address and the name of the mp3 to microsoft, WHETHER YOU HAVE CDDB ENABLED OR NOT. This is one way the RIAA finds illegal downloaders; thru microsoft. One irony is that since microsoft is always in bed with lawyers, they often get sued themselves as in the microsoft office injunction case. Twist of fate.
In reply to the tweaking applications, neither God Mode nor Rainmeter are actual tweaking tools, but more of "aids for tweaking tools." God Mode creates a shortcut to all the built in customizing features of Windows, and Rainmeter is a monitor that in a way helps to tell you if you're doing too much (meaning all the tweaks are bogging down your resources).
So while it is good that they were mentioned because they are helpful, it's not right to call them tweaking tools (or Applications as the article calls them).