I have a @mydomain.com and via Gmail Google Apps for business. It was down for 2 days so I did not receive emails that bounced from clients. Is there anyway to get those messages now that the email is back up?
The answer to this would completely depend on why the emails were bounced.
For example, if your MX records weren't pointing to Google's servers, no, this wouldn't be possible in Apps as the messages never hit Google's servers to begin with. You will need to reach out to any clients that you suspect received bounce messages and ask them to resend them.
Some DNS providers also offer email spooling services in the event of some DNS setting causing failures to deliver messages, etc. You would need to contact them to check on this though.
If the mails were making it to Google's servers but Apps was bouncing them for some reason, you can check the Email search log to find the bounced messages.