Unfortunately the chang of the font size is not yet possible from within Eclipse itself (for some of UI components like Menu and Navigator for example), at least for Eclipse version 3.2.0.
The UI font size can only be changed via the X resource mechanism. If you are using a gtk or gtk2 build, then the font size should automatically adapt to the settings of your theme or your personal preferences.
Use xfontsel to select a font. For example:
-misc-fixed-medium-r-normal-*-10-*-*-*-c-*-iso8859-1
Modify a config file: ~/.Xdefaults
Eclipse*fontList:-misc-fixed-medium-r-normal-*-10-*-*-*-c-*-iso8859-1
Use the following command to apply the font:
xrdb ~/.Xdefaults