When we started looking at Google Apps for our domain there was one thing that stood out that always irked me. There was very little space for domain wide customization. Sure, Google is working on making it easier with a new user management tool, widgets, etc but something as simple as quick links to our other services were no where to be found. After searching high and low, I came up with this solution and I hope it can help you out too.
The very first link we wanted in Google Apps was one to Postini, one of Google's own services for anti-spam. It's no where to be found in the web interface and yet people need access to it every day. This is where a bit of hacking came into play. I popped over to the Apps Marketplace (Google's new playground for third party developers). I paid the $100 to publish an app and began working on my non-app-app -- I'll explain that in a bit.
Go ahead and login to the marketplace and get over to your Vendor Profile so you can "Create a new listing". Make sure "My product may be directly installed into Google Apps domain" is checked off.

Choose a category (it doesn't matter which one), fill in a name, a summary and a full overview (again, these don't matter either) and put something into the "Pricing Summary" box. I typed, "It's free because it's mine" but you can enter anything you want.
Next it where the real process happens. Copy the code below into the "Manifest" box:
<?xml version="1.0" encoding="UTF-8" ?>
<ApplicationManifest xmlns="http://schemas.google.com/ApplicationManifest/2009">
<!-- Support info to show in the marketplace & control panel -->
<Support>
<!-- URL for application configuration, accessed from the app settings page in the control panel -->
<Link rel="manage" href="http://www.example.com/google/admin.php?domain=${DOMAIN_NAME}" />
<!-- URL explaining how customers get support. -->
<Link rel="support" href="http://www.example.com/google/support.php" />
<!-- URL that is displayed to admins during the deletion process, to specify policies such as data retention, how to claim accounts, etc. -->
<Link rel="deletion-policy" href="http://www.example.com/google/deletion-policy.php" />
</Support>
<!-- Name and description pulled from message bundles -->
<Name>Links - LiveMeeting</Name>
<Description>A simple application for testing the marketplace</Description>
<!-- Show this link in Google's universal navigation for all users -->
<Extension id="navLink" type="link">
<Name> ✮ Some Cool App Here</Name>
<Url>https://www.somerandomapp.com/someotherdir/</Url>
</Extension>
<!-- Declare our OpenID realm so our app is white listed -->
<Extension id="realm" type="openIdRealm">
<Url>http://www.example.com</Url>
</Extension>
</ApplicationManifest>
There are only two areas you need to be concerned about for our purposes. The first <Name> to </Name> section is what shows up in the Google Apps admin panel. I recommend calling it something that you'll remember later.
The second area, <Extension id=navLink" type="link"> is where you fill out what you'd like to show up to your users in the Global Navigation bar in Google Apps. Just fill in the values you want.
Finally, hit "Save and Preview". You should be taken to the "Review your listing" page. There's no need to publish it (The big GOOG will reject it anyway) but instead click on "Add it now" on the right hand side of the page and enter your Google Apps domain.
Follow the steps to add it to your domain, click through any approvals and make sure you you click to activate any licenses (sometimes it pops up with an error, just try again) until you see three green check marks in your admin panel.
And then you're all set. It takes about 15 minutes for them to show up for your users but you should see links (as you see in the screen shot at the top of this post) that your users can now click. You can add as many as you'd like (at least I haven't hit a limit) and they always show up in alphabetical order.
Let me know if this helps you out with your Google Apps roll outs and if you have any other cool tips or tricks to share, leave them here in the comments for others to try out.