Are there any ways to improve the font rendering in X11.app / XQuartz?
Warning: this is not my final answer, it will take some time to provide a better one.

Tested on OS X 10.8.5 with XQuartz 2.7.4 (xorg-server 1.13.0) and:


meld - installed via brew install meld
xterm
xclock


To tune the fonts create a file ~/.Xresources and put this:

Xft.dpi:        96
Xft.antialias:  true
Xft.hinting:    true
Xft.autohint:   true
Xft.rgba:       rgb
Xft.hintstyle:  hintfull

XTerm*faceName: DejaVu Sans Mono
*faceName: DejaVu Sans Mono


Inside ~/.gtkrc-2.0:

style "user-font" {
    font_name = "Lucida Grande 10"
}
widget_class "*" style "user-font"

gtk-font-name="Lucida Grande 10"
gtk-enable-mnemonics = 0


Feel free to post your modifications, as long they are using standard Fonts available on OS X, I would like to make this drop-in recipe. 

The last file has an effect on meld and other gtk apps.

Note, the font is the same as the one used in OS X UI but the rendering is still a little bit different.