I publish frequently from VS 2013 using web deploy, its important to note that vs will only publish files that are part of your project so if you exclude the App_Data/NuGetBackup it should no longer be deployed.

Additionally if you open Properties/PublishProfiles/something.pubxml add/update the line MSDeployUseChecksum to true, then this will change from the default check which is a simple file modfiied check (which is ok for solo developer but more than 1 and each dev publishes different file modified) to only files that have changed check.

<MSDeployUseChecksum>true</MSDeployUseChecksum>

The above settings might be specific to web deployed but alternatively...

The last option is unloading the project in VS then edit the proj file (so you see the xml) and you can explicitly exclude files & folder from deployment (http://blogs.msdn.com/b/webdev/archive/2010/04/22/web-deployment-excluding-files-and-folders-via-the-web-application-s-project-file.aspx)

<ExcludeFilesFromDeployment>file1;file2;file3</ExcludeFilesFromDeployment>

<ExcludeFoldersFromDeployment>Folder1;Folder2</ExcludeFoldersFromDeployment>