For trinity:
it sounds like the worldserver.exe relies on a specific DLL (more specifically a method within the DLL), most likely the program is trying to call something that is no longer there.
The registry is the main area these dependencies addresses would be stored, improper 'Cleaning' could have caused these issues (and I would think issues in other random programs on your computer)
For Arcemu:
Looks to be the same issue, they rely on a library that has not been copied into the directory, or its "Reference" in the registry has been corrupted.
My advice: Go through all of the "Setup" steps again, I'd recommend (but you can try without) re-installing Visual studio, re-downloading source or dependencies, removing dlls that need to be moved into the server folder etc.
Edit: Pretend Like You Are Starting Over
Last edited by shadeslayor; 02-13-2014 at 07:54 PM. Reason: Clarity
Ok thanks