Thanks a lot for reporting this, however I was unable to reproduce the behaviour you describe. When testing, I reduced the resolution of my display to 800x600 and opened a few of the default apps (Evince, EoG and Totem, Appearance and Displays), but was able to view the entire window each time. What I did notice was that some apps were opening in fullscreen mode, which I assume is what they are designed to do when their default window size exceeds that of the current display.
I notice that Ubuntu Netbook Remix has been included in this report. UNR was running an older version of Unity and the Gnome 2.x stack, whereas Ubuntu 11.10 now runs Gnome 3.x and a radically updated version of Unity, and UNR has since been discontinued.
Can you please confirm whether or not you are still affected by this bug on the most up to date version of Ubuntu?