Recent versions of Subclipse have added a feature to the Synchronize view called "Show Out of Date Folders". This can be toggled on/off via an option on the view menu and also in the SVN Preferences. It is on by default, and I'd recommend you leave it on. The feature is a response to problems that are created for the user by Subversion's mixed revision working copies feature. See my previous post on that topic for more details and some of the issues you encounter when working with mixed revision working copies.
Historically, the Synchronize view has shown similar output to what one would get if they ran the svn status -u command. With the exception of folder adds and deletes, the svn status command will only include a folder in the list of incoming changes if the properties on the folder have been changed in the repository. However, as my previous post on mixed revision working copies articulates, if any file anywhere beneath the folder, or its children, has been modified, then the folder's revision will also have been incremented within the repository. Consequently, that means that your local copy of the folder is out of date as far as Subversion is concerned. Generally this is not a problem as most day to day activities do not require your folders to be up to date. However, there are several types of changes that you cannot commit unless the folder is fully up to date. Examples of these are if you perform an operation such as setting properties on the folder or if you want to delete or rename/refactor the folder. If you perform one of these operations, then when you try to commit the change, the commit would fail because the folder is out of date.
Just to reiterate this again, every time you commit a change to the repository, all parent folders (all the way back to the repository root) of the items you commit have their revision bumped in the repository. However, the revision of these folders in your local working copy is not bumped by a commit. The folder has to be updated with svn update in order for this to happen. This has caused a lot of confusion with users, especially since the Synchronize view should theoretically show them this.
Well, with the addition of this feature, it now does.
There was a second reason the feature was added, and that was to make update work better -- to allow the Synchronize view to help the user correctly update the folder revisions in their working copy. The Synchronize view is kind of a strange animal, although I cannot think of a better way it could work. When Subclipse populates the view, we are giving it the list of resources that are incoming or outgoing, based on the output we get from running the Subversion status API. The view then uses that list to construct the UI. If you are familiar with the view, you know that it is a tree-like view that shows the folder structure.
Since Eclipse adds the tree structure to make the UI look right, many of those tree nodes are not really there. What I mean by this is that when you select something like the tree root and choose the update option, the Subclipse code that is fired then has to ask Eclipse what you selected so that it can process the option. Eclipse gives back only the resources Subclipse gave it when the view was created, based of course on what you have selected. Subclipse does not receive back the tree nodes that Eclipse created for the UI.
We tried several techniques where we would figure out the UI element you selected and then try to do the right thing, but nothing ever worked perfectly. What worked best was to just update the resources that Eclipse told us you selected. However, this is where the update problem surfaces. Since svn status -u typically does not include folders, Subclipse typically never receives folders as items to update. Consequently, when you would run update from this view, your folders would never get updated and would always be out of date. This feature fixes this problem, as folders now show up as changes and therefore are included in the selections. This has allowed Subclipse to resolve all of the issues we have fought with on getting update to work the way we want from this view.
Of course, there is something of a negative side-effect to this feature too. Namely, that most the time you do not really want to see this extra information. Also, after you commit some files, you are always going to have incoming out of date folders (because that is how Subversion works). There really isn't any way around this. The folders are out of date after a commit, so the view shows them. Now that Subclipse is giving you all the information you need, you are at least armed with the information you need to decide when you want to update those folders.
Update: I rewrote the 2nd paragraph into what is now the 2nd and 3rd paragraph in an attempt to explain this more clearly. It is definitely a hard thing to explain clearly.