A possible solution now is to use code in userChrome.css
The order of toolbars can be changed by setting the value of the -moz-ordinal-group property of that toolbar. You can open the Firefox > Web Developer (or Tools) > Error Console and click the Clear button to clear the display. Copy and paste this code in the Code field and click Evaluate. That will display a list of the currently install toolbar with their -moz-ordinal-group setting. Toolbars added by an extension have a value of 50 and making one smaller makes it appears as the first and making it larger appear as the last in the list.

EDIT:
Note that current Firefox (24 and later) releases no longer have the error Console, but have the Browser Console (Firefox/Tools > Web Developer) that has a command line where you can paste the code and press the Enter key to run the code. If the command line is hidden then set the devtools.chrome.enabled preference to true in about:config, or set the "Enable chrome debugging" option in the developer tool settings.

• https://developer.mozilla.org/Tools/Browser_Console#Browser_Console_command_line
• http://www.robodesign.ro/mihai/blog/the-browser-console-is-replacing-the-error-console

var Cc = Components.classes, Ci = Components.interfaces;
var wm = Cc["@mozilla.org/appshell/window-mediator;1"].getService(Ci.nsIWindowMediator);
var mw = wm.getMostRecentWindow("navigator:browser");
var doc = mw.document;
var nav = doc.getElementById('navigator-toolbox');
var elm = nav.getElementsByTagName('toolbar');
var i, inf='',moz='-moz-box-ordinal-group';
for(i=0;E=elm[i];i++){ inf+='#'+E.id+' { '+moz+': '+doc.defaultView.getComputedStyle(E,"").getPropertyValue(moz)+' }\n'; }
inf;

Only add the modified line(s) to userChrome.css below the @namespace line.

@namespace url("http://www.mozilla.org/keymaster/gatekeeper/there.is.only.xul"); /* only needed once */

• http://kb.mozillazine.org/Editing_configuration
• ChromEdit Plus: http://webdesigns.ms11.net/chromeditp.html

EDIT: Forgot to write that you need to add the !important; flag to override the current property value.

{ -moz-box-ordinal-group: 30 !important; }

I just upgraded to Firefox 4.0 and edited my "extensions.ini" file in order to move the Google Toolbar to the bottom.

Navigate to Firefox Profiles folder: C:\Users\[username]\AppData\Roaming\Mozilla\Firefox\Profiles\[something].default\

Open the file extensions.ini

You'll see lines that look like this:

Extension0=C:\Users\[username]\AppData\Roaming\Mozilla\Firefox\Profiles\[something].default\extensions\autopager@mozilla.org

Extension1=C:\Users\[username]\AppData\Roaming\Mozilla\Firefox\Profiles\[something].default\extensions\elemhidehelper@adblockplus.org

Extension14=C:\Users\[username]\AppData\Roaming\Mozilla\Firefox\Profiles\[something].default\extensions\{CB56AAF9-68C8-41bd-8E5C-7B53232CF7B9}

Extension15=C:\Users\[username]\AppData\Roaming\Mozilla\Firefox\Profiles\[something].default\extensions\{d10d0bf8-f5b5-c8b4-a8b2-2b9879e08c5d}

Each line identifies the location of the extension, but not necessarily the name. To identify an extension navigate to it's listed location and open the Chrome folder to see its name.

When you find the one you want to move use copy and paste to move it up or down the list and then renumber the lines accordingly. In Firefox 4.0 the list is loaded in order (as opposed to 3.0 and earlier when it was reversed). So if you want the Google Toolbar to be at the bottom it should be the last on the list.