I have a lousy old monitor with a 1024×768 resolution and I’m using Mac OS 10.4 (Tiger). When I installed the new Gimp, the Toolbox window was too tall. On a Mac, you can only resize windows by dragging their lower right corner. Unfortunately, the lower edge is not visible if the window is too tall.
I tried using Quartz Debug (/Developer/Applications/Performance Tools/Quartz Debug.app) to switch the User Interface Resolution to values smaller than 1.00; the result is that any new applications you start have their user interface scaled appropriately. But although the X11.app user interface is scaled, the windows of the applications running within it are not! That’s why any suggestions involving monkeying around with these settings such as defaults write -g AppleDisplayScaleFactor 0.8 for a global temporary solution or defaults write com.apple.SystemPreferences AppleDisplayScaleFactor .75 for a permanent per-application default and their ilk will not work.
I then compiled and installed wmctrl to change the window size from the command line. But it doesn’t support the Apple window manager, quartz-wm – wmctrl -l will print the help text instead of a window list.
What I ended up doing was compiling and installing the simplest window manager I know, Blackbox.
In your /.xinitrc:
/usr/local/bin/bsetroot -solid midnightblue exec /usr/local/bin/blackbox
You must specify the full path to the binaries. That confused me for a while!
Once you’re in Blackbox, create a new xterm window, and use wmctrl -r Toolbox -e 0,20,20,300,500 to resize the window. You can get the names using wmctrl -l.
You can use ⌘N to create a new xterm window. If you’re using X11.app and the default window-manager (replace blackbox with quartz-wm in your .xinitrc file), you can change these keybindings. Or just use ⌘click on the background to call the Blackbox menu.
To edit the Blackbox menu, I suggest you just sudo chown <yournamehere> /usr/local/share/blackbox/menu and edit the file directly, commenting out all the applications you won’t be using.
If you’re using X11.app and the default window-manager (replace blackbox with quartz-wm in your .xinitrc file), you can change the X11 default such that it always starts in full-screen mode, ie. it has a root window. Remember to use ⎇⌘A to switch away from X11. The bgetroot command im my .xinitrc just makes sure I’m not getting the terrible default black & white X11 background.
Good luck. 
Possible pitfalls: