Create a file named, say, gtkrc-eclipse:

style "eclipse" {
font_name = "Sans Condensed 8"
}
class "GtkWidget" style "eclipse"

Then set a certain environment variable when invoking eclipse:
$ GTK2_RC_FILES=gtkrc-eclipse eclipse

via eclipse – How can I configure the font size for the tree item in the package explorer in ecilpse – Stack Overflow.

And to change the font size for the irritating tabs, you can edit the CSS

If you take a look in ECLIPSE_HOME/plugins/org.eclipse.platform_4.2.0.v201206081400/css, you will find the different CSS used. On Linux, if you use the GTK style (in the Preferences/Appearances), the e4_default_gtk.css is used.

Edit this file and change the .MPartStack section :


.MPartStack {
font-size: 9;
font-family: "Droid Sans";
swt-simple: false;
swt-mru-visible: false;
}