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So, pretty basic question,

I use for some work email, I use multiple Google Apps emails for different things.

I don't use an email client, I just use the different webmail interfaces,

What I am hoping I can find is an email notifier that can check emails, and multiple Google Apps emails and gives me a notification?

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Can you try if popper works for you. – Abhay Rana Apr 24 '13 at 9:13
@Capt.Nemo How do I install it? add the ppa:ralf.hersel/rhersel-ppa ppa is returning a 404 on apt-get update – Hailwood Apr 24 '13 at 11:23

I would set it up like this:

The Google Apps Mail

Instal unity-mail & unity-webapps-gmail

sudo apt-get install unity-mail unity-webapps-gmail

Open Unity mail and configure it for Google Apps. Setting it up is almost the same as for a gmail account, except for the username which is

You can even set it up with URL so that when you click a mail under the message notification tray you will go directly to the inbox...

The mail

Unfortunately does not support IMAP yet, so I would set up forwarding to a gmail account I would create only for this purpose and then set up a second account in unity mail..

Alternatively you can use extentions for your browser:
If you are using chrome go for notifier
And if you use Firefox: X-Notifier

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