I have a .NET solution which was badly organised, so I moved some projects around to appropriate folders. In the solution, I simply fixed the paths to the new locations, and everything is working in my working copy.
I used AnkhSVN to commit the solution to the repository, which worked out fine as well.
However, when I look in the repo explorer, the folders inside are organised in the old way.
What do I need to do?
If you are using Visual Studio you are not creating folders but filters. Filters basically allow you to organize your solution visually but in the background the folders will stay in their original location.
Subversion uses metadata files in your solution folder structure to keep track of where stuff is, and where it maps to in the repository - these files are typically held in .svn or _svn folders in each solution folder and subfolder. Even though you may have physically moved things around in your working copy, those metadata files still point to the original structures in the repository.
What you could do (and please, anyone with deeper Subversion knowledge than I pipe-up if there's a smarter / better option) is re-organise the folder structure in the repository through RepoBrowser. Once you've got things where you want them in there, you can check-out a new working copy. The metadata files will then reflect the new repository structure.