I've been testing various mail notification systems for Google Apps. Mail notification systems are small utilities that tap into your Google Apps mail account and ping you with either a visual cue, a sound bite or both. Most of the time I have my Chrome browser up and running with multiple tabs and one of those tabs always has my Google Apps mail - however, other than the mail count description on the tab, there's no type of indication that I've received new mail. Each of these utilities has its own pros and cons - so select the one that meets your needs and enjoy.
Sohail's Gmail Notifier for Google Apps
 website: www.gmailnotifier.net
pricing: $7.99 for pro and $13.99 for multiple accounts
Sohail's Gmail Notifier for Google Apps works in many ways like Google's own notifier (the one that works ONLY with Gmail) with the exception that it works with Google Apps as well as some nice optional features. Technically, the application works by reading the XML from Gmail's atom and displays the message (note that currently Google only posts 20 unread messages in the atom).
Initially, I had some difficulties loading the application on 64bit Vista (no surprise, eh?) - but a quick reply by the developer helped me out - essentially, what's necessary is that you need to setup the program to run in administrator mode - this is easy to do - after installation and before starting... simply find the program, select properties, select the Compatibility tab, and check the box Run this program as an administrator.
Once started, setup is easy as selecting a couple of options:
Startup options allow the user to set the application to startup on system start (along with options for this user only or all users).
Check mail options allow the user to select the frequency of pinging the Google mail server - the options are once every 15 second up to once every 15 minutes.
Show message option allows the user to select a length of time in seconds from 1 to 5 seconds. I like 5 seconds - that gives me enough time to actually read the subject and the brief intro to the contents of the notifier.
Notifier skin allows the selection of various colors - blue, brown, green, orange, purple, red, and yellow.
Transparency setting by percentage determines how much of the currently open application displays under the notification message. I like 30% as that allows me to continue viewing what I'm currently working on as well as read the notifier.
Reset custom position to default - the default position for the notifier is a rectangular box that appears in the bottom right corner of your display - the user can move the notifier position to anywhere on their display - however, if the user decides they want the default position, then checking this box returns the notifier back to the bottom right corner of the display.
Sound settings allow the playing and selection of a sound notifier. During my testing I could not get the sound selection to reliably pick up a custom wav file for playback - I sent an e-mail to the developer and will update once I find a solution.
Change login allows the section of either a gmail or a google apps account and a password setting. There is a multi account version of the notifier. I originally tried testing the multi account version but had problems with setup - most likely this is a 64bit Vista problem - I've sent an inquiry to the developer and I'll update once I find a solution. Supposedly, all other versions of Windows including XP and 7 do not have problems (32bit Vista probably isn't an issue either).
The mailto/proxy settings tab has an extremely important function; upon mailto selection, the notifier will register as a mail client to the operating system - this will allow the user to click on an email (such as at a website) and shoot a message through Google Apps!
Sohail's Gmail Notifier for Google Apps in action works rather well. Upon receipt of an email, the notifier will appear in the bottom right corner of the display and ding the audio queue to receipt of mail. The notifier displays the time, email sender, subject, and a brief intro to the message. Selecting the notifier causes the browser to open directly to the message. Options take the user to their inbox, check for messages, tell me again (which shows all the unread mail again), and compose an email. Additionally, now when I'm at a web page with an e-mail address (those with a mailto:), selecting the email address brings the mail address into a new Google Apps email.
Gmail Notifier
 pricing: free
Installation of the application was a breeze - a simple download and install. Preferences for this client are limited to simply turning on/off the various features - sound alert, tray icon blink, utilization for mailto, and running at startup are the main features users will want to turn on - in fact, I selected all options available. Additionally, the user can select their own wav file for an audio queue.
Gmail Notifier is easy to setup and simple to use - the most important point to realize is that Gmail Notifier is an imap client - that means that the user will need to go into their Google mail settings and turn on imap access. Setting up multiple Gmail or Google Apps accounts is as easy as entering in your user id and password.
Upon notification, the user selects the tray icon which pops up the notifier - the notifier initially displays the email sender and the subject but skips out on displaying any of the actual message. However, the user can select the message and the entire contents of the email will display - this is because Gmail Notifier is really an imap client. In addition to reading the complete message, the user can mark the message as read or delete the message completely. Surprisingly there are two functions missing - the first being a way to reply or open the message in the browser - and second, the ability to archive; a quintessential function of Google's mail system as is its vast storage potential (why delete when you can archive) and Gmail Notifier doesn't tap into this capability.
Finally, my main complaint of Gmail Notifier is how it incorporated the mailto feature. There currently is not an option to select a default mailto account, instead the application intercepts the mailto request and opens the browser to the generic gmail page - that's not even useful to those using Google Apps. A minor grievance is while the developer's website says it's spamware free - it does have links to Amazon search and Google search which drives credit back to the developer (explains why the pricing is free).
Google Talk Client
 pricing: free
Google's Talk Client is a compromise when it comes to acting as a notifier for Google Apps mail and falls short in many categories. Like Sohail's notifier, Google Talk Client works by reading the XML from Gmail's atom and displays about the first 75 characters of the message in a notifier box that pops up in the bottom right of the display.
Installation was quick and simple - upon installation the application asked for my user id and my password and then proceeded to let me know I had unread mail.
However, Google's notification feels like a last minute bolt-on to the Google Talk client - as if the product manager was forced to throw something on that they didn't really want. The various settings related to mail notification are scattered throughout the setup tabs and are very limited.
What is available are on/off settings for automatic startup, mailto incorporation, and show notification window. That's it!
What's lacking - quite a bit - multiple gmail and Google Apps accounts, frequency settings to ping the server (although my experience is that mail notification is instantaneous - even to the point where it displays prior to the browser), notifier display time (it's about 3 seconds), any type of skin variation or transparency, ability to move the notification anywhere other than the bottom right corner, and sound settings of any type (does NOT make an audio queue upon new mail receipt). Essentially what you receive is a bare bones message notifier.
On the positive side - it works, its very quick, and the mailto functionality works like a charm!
Conclusion
While each version has its own pros and cons - there's enough functionality in each application to suite individual needs, desires, and cost point. I've put together a small matrix outlining the major points of a notification system along with my observations.
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