Since I run my own web design business and I am a youth pastor at our church, I have multiple Google Apps accounts for each entity. This suddenly became frustrating because I was using Apple Mail for both accounts, but was frustrated with Apple Mail's inability to delete emails off of the Google Apps server when pulled. I personally do not like the nuances of IMAP though in some circumstances it is best.
I then reverted back to Google Notifier for Mac, but you are required to hack the app to install a second one on your Mac because it only notifies for one gmail or google apps account at a time. This was also frustrating, I was seeing my church emails entirely too late to be worth anything, relying on my iPhone to chime in to get my church emails while sitting at my desk.
I performed a quick google search and found my answer... Notify Pro 2.1 for Mac. You can setup to 5 accounts of multiple types including Google Apps and GMail. I went for the Pro since it was only $9.45.