After upgrading from Notes client 5.0.8 to 6.5.5 I am no longer able to drap and drop messages from the Inbox to sub-folders. The work around is to expand the folder list then drag the email to the designated sub-folder.
Subject: Drag and Drop in Folders
If you mouse over collapsed folder the subfolders should expand so you can drop a doc into a subfolder. Sometimes you need to hold it there for a moment before the folders expand.