Can I change the font systemwide (10.8.3)
Here are the corresponding hidden preferences:

defaults write -g NSSystemFont LucidaGrande
defaults write -g NSSystemFontSize -int 13
defaults write -g NSBoldSystemFont LucidaGrande-Bold
defaults write -g NSBoldSystemFontSize -int 13
defaults write -g NSFont Helvetica
defaults write -g NSFontSize -int 12 
defaults write -g NSFixedPitchFont Menlo-Regular
defaults write -g NSFixedPitchFontSize -int 11
defaults write -g NSMessageFont LucidaGrande
defaults write -g NSMessageFontSize -int 13
defaults write -g NSLabelFont LucidaGrande
defaults write -g NSLabelFontSize -int 10
defaults write -g NSToolTipsFont LucidaGrande
defaults write -g NSToolTipsFontSize -int 11
defaults write -g NSTitleBarFont LucidaGrande
defaults write -g NSTitleBarFontSize -int 13
defaults write -g NSPaletteFont LucidaGrande
defaults write -g NSPaletteFontSize -int 10


They don't affect windows shown by processes owned by root, like the force quit window. sudo defaults write -g (which modifies /var/root/Library/Preferences/.GlobalPreferences.plist) affects only them.

There is no way to change many fonts (like the font used on the menu bar) and text elements are not aligned correctly when using different fonts. You can also replace Lucida Grande.ttc with some other font.