This is about the worst design flaw / bug /emergent interaction I’ve encountered in the past few years.
Here's the story from my rejected post to the Appigo Todo Google Group 
When I added Notebook to Todo, and after I'd imported hundreds of notes Toodledo, I ended up with a set of categories (aka folders) for my iPhone Appigo Notes and Tasks that were the sum of the Palm categories I had used for Notes and the Palm categories I had used for Tasks.
Since my Palm Notes and Tasks had different categories, there were empty folders that showed in Notes (but not empty in Tasks) and vice-versa. They cluttered up my folder list.
So I deleted the empty folders on both sides.
Can you guess what happens next?
It took a surprisingly long time after the deletion, perhaps due to Toodledo synchronization issues, but I now have hundreds of Tasks and Notes that no longer belong to any category…
… At least when synchronizing with Toodledo, Tasks and Notes share a common set of categories/folders. If you remove a folder from Notes that is empty, you remove the matching folder from Tasks. All contained Tasks go into the inbox (at least they aren't deleted).
This is the single worst bug or design flaw or bizarre emergent synchronization behavior I've run into in several years. I don't know how I'll sort this out.There’s no way to undo this behavior, and there’s no good UI on either the iPhone or Toodledo for manipulating sets of Tasks or Notes.
Man, do I hate synchronization.
What a bloody mess.
Update 11/9/08: To clarify why the problem is so bad. If the data lived in Outlook, this would be a nuisance problem. It would take some time, but I could select swathes of items and assign them to new categories. Neither Appigo nor Toodledo support multi-select operations.
I did some further testing. I created a folder in Toodledo tasks, and verified it did not, at first, appear in Toodledo Notes. I did the same with Toodledo notes. However after Appigo Notes synchronization, the Toodledo TASKS folder appeared in Appigo Notes. After a cycle of Appigo Tasks and Notes synchronization the new Toodledo Notes and Tasks folders appeared in both Appigo Tasks and Notes and then synchronized back to Toodledo Notes and Tasks.
Which brings me back to two critical points I keep relearning:
- Synchronization is Hell.
- Reliable service requires a single vendor to control the client and the server. Differences in folder models between Toodledo and Appigo are at the root of this exquisitely nasty bug.
- There is a vast and perhaps unbridgeable gap between the capabilities of a robust desktop client like Outlook and what the Cloud can offer.
I suspect Toodledo stores notes in the same tables they use for tasks, hence the shared categories.
So this is an example of an emergent bug arising from synchronization between different application models.
Everything I need to know about Health Care messaging and synchronization I learned from my PDAs.
Update 11/13/2008: I looked into alternatives to Appigo such as Things.app and OmniFocus. The first is pre-release and has no import/export capabilities and the second, though released, has no useful import/export capabilities.
Neither meets my minimal data freedom requirements.
Since the category-loss bug arises from the combined use of Appigo's Todo.app and Notebook.app synchronizing against Toodledo's single Task/Note store, one workaround is to keep Todo.app and Toodledo Tasks but look for another solution for Notes, such as Evernote.
Alternatively, since Evernote now has a published API, Appigo could use Evernote as their note store instead of Toodledo. Their Notebook app is far more stable and useful than the Evernote iPhone client.
I'd suggest this to Appigo, but the last post I submitted to the Appigo support Group was not published. 
I don't have better options for the moment, so I'll stick with Appigo iPhone Todo.app and Notebook.app for the next few months. Things.app may be ready for my use by February 2009, assuming they have a robust set of import/export capabilities on the client.
Of course Google could create a Task companion for Google Calendar at any time. If they do that then the deck will be reshuffled and we'll have more options. I don't expect any solutions from Apple; I think they're in much worse organizational shape than we realize.
 Appigo declined to publish my post to their Google Group based support forum. If my most recent note on this thread doesn't appear, I'll have to conclude that Appigo is aggressively censoring their customer posts -- at least on this very sensitive topic.
Update 11/13/08: My posts are not appearing in Appigo's Google Group.