Xcode 4 "Clean" vs. "Clean Build Folder"

If you select Clean from the Product menu, XCode will delete the files inside every folder in the Build folder, if you select Clean Build Folder it will delete the entire Build folder.

After Clean command:

After Clean Build Folder command:

I think you should select Clean Build Folder when you want to build a binary that you want to release to the AppStore, when you messed up with your project or when your app doesn't work for an "unknown" reason, otherwise use Clean.

I hope I've answered your question :D

Clean… cleans the folders for the current selected target.
Clean Build Folder… cleans the folders for all the targets.