How do you remove SSL certificate exceptions on iOS?
You can delete the SSL certificate.
Go to Settings → General → Reset → Network Settings.
This resolves the problem.
[EDIT]
As of iOS 10.3.2 this does NOT work. Instead it wipes out your network settings, but does NOT remove certificate exceptions.
I found a nice blog post that gives some good information and tips regarding ssl certificates.
Once the SSL exception is added there doesn’t seem to be a way to remove it in iOS 7. In previous versions going to Settings->Safari and selecting ‘Clear Cookies and Data’ would delete it. This no longer seems to work in iOS 7....
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To remove the SSL exception on Safari on iOS 7.0.4 you can reset all settings (General > Reset > Reset Settings). Unfortunately it deletes all your settings (go figure); but it's one huge step better than a full restore that makes you lose your text messages.
I found instructions on how to do this in iOS 6 here and also here with pictures. This probably also works in iOS 5 but I cannot confirm (the Profiles page mentioned below likely doesn't appear until there are installed certificates to view or delete). See information about how this changed iOS 7 below if this doesn't also work there.
Remove Security Certificates
from the first link above:
Turn on your iPhone and click on the "Settings" icon in the main menu screen. Select "General" from the list of options that appear in the drop-down menu.
Select "Profiles" from the list of options that appear and a list of all the certificate on your iPhone will appear on screen.
Scroll through the list of certificates until you come to the one you would like to remove from your iPhone and click the "Remove" button on the screen. The certificate will then be removed. Repeat the process for any other certificates you would like to remove.
You can also manage certificates with the Apple Configurator in Mavericks, the iPhone Configuration Utility in Mountain Lion, Lion and Snow Leopard, and there is a Windows version. There are instructions available.
Information on how this changed in iOS 7.
SSL Detective
From my comment above, check out SSL Detective for iOS. As far as I've seen, it's the only iOS app of it's kind, and may help you determine which certificates you'd like to delete.
Another one for SSL Detective. For some reason the last iOS 6 compatible version of an app I use daily suddenly stopped working with an Untrusted Root Certificate error saying "The authenticity of "GeoTrust Primary Certification Authority - G3" cannot be verified." I could have used SSL Detective's "Email Certs" feature to just install the cert and trust it myself, but that wouldn't have gotten to the ROOT Cause of the issue. (no pun intended)
The necessary Root Certificate was found here: I browsed that website from Safari on my iPhone and clicked to install the G3 (SHA256) root certificate and it totally solved my problem.
Also, this GeoTrust utility will come in handy for future readers to verify the website they're visiting has correctly configured SSL in the first place: SSL Certificate Checker