How to apply GTK changes only to eclipse:
Somewhere on your home directory, create a gtkrc file (like: ~/.gtkrc-eclipse) with following content:
gtk-color-scheme = "selected_bg_color:#0AFC02\nselected_fg_color:#FFFFFF\norginal_selected_bg_color:#f07746\ntooltip_bg_color:#f5f5c5\ntooltip_fg_color:#000000"
Launch eclipse from command line like,
env GTK2_RC_FILES=/usr/share/themes/<Your current theme>/gtk-2.0/gtkrc:/home/<user name>/.gtkrc-eclipse '
env GTK2_RC_FILES=/usr/share/themes/Ambiance/gtk-2.0/gtkrc:/home/chandrayya/.gtkrc-eclipse '/opt/eclipse-3.3/eclipse'
You can find out your current theme by executing,
gsettings get org.gnome.desktop.interface gtk-theme
Choose your fg/bg color code.
Also refer this post Change Eclipse sidebar vertical scope highlighting.