In the projects I work in, it seems the biggest problem with Merging changes is in the Windows Forms/GUI changes. We use Araxis Merge to compare the changes, but it can be hundreds of changes per file. And you have have to make notes and/or rename items to make sure you know what you are merging.
A big problem is if developers allow new controls to use the default names. Then there will end of being, for instance, 2 Label220's. Then the merge will merge half of the code together, but leave other parts separate; this basically just breaks the GUI.
Are there any tools for merging .NET (Windows Forms) GUIs better than at a code level?
We use Subversion. Is Mercurial any better at this?