I use the keyboard shortcuts extensively (I very rarely ever reach for the
mouse, except for the web browser), and the common spots I've run into where
the "global" keyboard shortcuts are "inhibited" are primarily when the focus
is in a Java/Javascript/Flash "plug-in". This happens most commonly in the
browser, and the easiest way to regain control is to move the focus away from
the plug-in, which you can (yes, without reaching for the mouse) do by typing
Ctrl+D, which places the focus in the Address Bar of the browser (this works
for Netscape Navigator, Mozilla, and Firefox). You can then type Tab to move
the focus to the document window, which leaves the browser window in a useful
state when you return to it later. Then, the Ctrl+Alt+N typically gets your
Notepad to launch/switch-to.
There are a number of places in Windows 2000/XP/Vista where user
interactions are being managed through a plug-in (possibly Java/Javascript or
ActiveX control perhaps) but you're not "formally" in a web browser, and you
wouldn't know it, except that a number of keyboard shortcuts abruptly stop
working for the duration that the plug-in has focus.
This is actually one of the biggest reasons that I dislike Java/Javascript
when I encounter it -- I'm *forced* to resort to using the mouse, when I find
unacceptable. I discover problems of this nature (particularly "tab ordering"
problems in dialogs and pop-up windows) precisely because I'm so
keyboard-centric in my computer use.
It sounds like you may be experiencing a different problem, but this
scenario comes up so often that I felt it worth documenting.