You're not the only one. It seemed to go away on its own for a couple instances, but one was completely persistent: my mom's 2010 Mac mini 2.66. Tried everything to fix it for her a couple times in the past two weeks when I had the chance and nothing worked, even a clean install. Finally came across this online, and that did the trick. Apparently, there was a bug in 10.7.4 that can mess up the System Root certificates, and it carries over clear up to 10.8.2 if you never fixed it manually.
I spent about 30 minutes last night manually changing certificate settings until nothing was listed as custom anymore, and presto, Mac App Store is again functional.
Here's what I used:
I solved this on my wife's computer by resetting the security certificate settings. This might help others:
Close all windows.
Keychain Access -> click on System Roots on the left, and then click on Certifcates on the bottom left.
Check to see if any of the certificates on the right have the blue "+" symbol - this means they have custom trust settings.
There is a bug in changing the policies, so you'll have to change them via the method below. Changing them just by changing the access to "system defaults" doesn't seem to save. The method below worked for me.
Double-click on each certificate with the custom setting (blue "+"), expand the section labled "trust". Change the "Secure Sockets Layer (SSL)" setting to "no value specified". Close window - you should be prompted for the password. Double-click on the certificate again, expand trust, change the "When using this certificate" setting to "Use System Defaults". Close window, and re-enter password.
If you didn't re-enter your password upon closing the window, the setting didn't take. The blue "+" should disappear after a few seconds when it's set back to default. Once all of the certificates are changed back to default, restart Safari.
This solved all of the problems for my wife's computer with these issues and OSX 10.7.4