Application windows do not fit on the screen

Not fitting in 1024x600 with reasonable leeway for panels should be considered a bug in the applications. Please file those bugs!

As Takkat said, you can usually alt+mouse drag the window to work around the bug. Additionally most window managers also have a 'move' action in the window menu that lets you move it with the keyboard.

Finally you can use xrandr to scale the window; for example,

xrandr --output LVDS1 --scale 1.2x1.5

would scale you to 1229x900. Crude, but effective.

If you use this last method, note that all the drivers I've tried this with get confused unless you go back to 1x1 before trying new ratios.