We've been having some problems with duplicate apps recently. One source has been appfresh users not being able to identify the apps on their mac. We have been working together with the excellent people over at metaquark to solve this issue, and we think we've come up a pretty neat solution. We now alias the old name to the app whenever we merge or rename an app, so that you get a warning when you try to register that app later.
This is how it looks:

We also redirect any requests for /app/



Is there any way to create aliases? Ex: For this one: http://osx.iusethis.com/app/doublecommandpreferences
There is a thingy at:
http://osx.iusethis.com/app/merge/1849
But I probably cannot use this (get a 404 when I enter something)
Yeah, that’s not open for end users. I used it to create that alias tho.