One of the key issues was the lack of documentation from the apps that have a custom scheme. In many instances this stops developers from being able to fully integrate their apps.
To help combat this issue, a ticket has been raised on UserVoice to add the ability to track custom scheme documentation within the DevCenter.
If you're a developer or would like to see people building apps that work together better I encourage you to vote.
At the moment the only real central place for this documentation is on the Nokia Developer Wiki.
There was also an attempt to build a list at GeekChamp but this appears to never have really taken off.
Neither of which is as good a solution as is now proposed.
p.s. And as a follow up to yesterday's list I'm now intending to try and create a more complete one based on the entire store catalogue. Hopefully this will be available in a few days.