I totally agree. It's worst when I'm playing on someone else's keyboard and expect to hit Alt and find some pointless Windows key making my start menu blink in the foreground and overloading my video card.. Luckily, with some VOIP software you can map the windows key to a command and block Windows from interpreting it.
As to the thread question.. It really depends on the applications you use, but I definitely appreciate having a few spare buttons around for mapping. For instance, while running TeamSpeak I use Pause to mute speakers, XFire I believe uses Scroll Lock + X for in-game functions, et cetera. The most valuable (non-alphanumeric) buttonset on my keyboard is definitely music controls. But there isn't really a key I don't use. Page Down? Yeah, the keyboard scroll wheel is what I use for that..