Is it possible to detect any certificates not packaged by Apple? I recently received a Mac and connected to my employer's network. When I connected, my Mac (not browser, it was in the connection dialog) asked me to do something with a new certificate. I accidentally clicked yes before I got past the title, and am worried I installed a root cert that allows my employer to see my encrypted traffic. Is there any way to check for any installed certificates not put there by Apple?
Chances are you installed the certificate that was required by your employers network.  For example at my work place we have 802.1x authentication on our Wifi, basically users log in with their normal username and passwords instead of a pre-shared Wifi key.  When they log in they must accept a certificate from our servers.

This doesn't necessarily mean that your employer can see your encrypted traffic, however it is very possible.  It depends what kind of infrastructure your employer has, i.e. do they have a system that does SSL inspection?  You won't know unless someone in IT tells you.

You can view the installed certificates through Keychain Access (Finder --> Utilities --> Keychain Access).  For my 802.1x Wifi there is a certificate in the 'Certificates' section at the very bottom of the left column (not the My Certificates).

Never-the-less you will be able to see all installed Certificated here.