I found today that I suffered the same issue on my 3rd generation iPad running iOS 6.0. My solution, while a bit drastic, was to go into Settings->General and choose Reset All Settings. After the settings got nuked and the device restarted, the problem was no longer present.
This reset didn't nuke my data, just WiFi settings and a few other things. The only annoying thing is that I had to choose a new passcode as our Exchange server settings wouldn't let me use my existing passcode for the device.
I hope this helps someone.
Before posting my question yesterday I went through all the various resetting and rebooting options and nothing worked.
Yesterday evening I noticed that AppZapp Pro was now working but AppFree HD was not. The links to the App Store in Apple's web pages also refused to work correctly.
This morning AppZapp Pro, AppFree HD and links in Safari all appear to be working as they should be. I did not make any further changes or reset anything else on my iPad 3 running iOS6 so I can only assume that the issue was with the Apple servers rather than a problem within the iPad itself and that overnight it was sorted out.
Thanks to all those people who who contributed with help and advice.