Make your Dock be flush against the corner of the desktop, instead of centered vertically or horizontally. This means your icons will stay put, regardless of how many windows are open:
defaults write com.apple.dock pinning -string start ;
killall Dock
Turn off menubar transparency on 10.5:
sudo defaults write /System/Library/LaunchDaemons/com.apple.WindowServer EnvironmentVariables -dict CI_NO_BACKGROUND_IMAGE 1
and then reboot (logging out isn’t enough). [Link]
via DaringFireball
update: Or just download TinkerTool