You can use GTK themes. For Gnome 3 Flashback I use clearlooks, but you can use GnomishDark for dark colors.
To make Eclipse using it, create script with name like eclisec.sh with following command:
GTK2_RC_FILES=$HOME/.themes/<your-theme-gtkrc-file> exec ./eclipse
and place your theme to $HOME/.themes/.
You can see my eclipse with GnomishDark theme here.
Also take a look at this article.