A user named kohlmannj at the indispensable macosxhints figured out how to use an app at the ADC site that can actually remove 3rd party sync items and reset your .Mac syncing to a 'never synced before' status. The hint is actually very simple to implement, but be sure to read the entire post to understand exactly what you're getting yourself into. In summary: this tool and hint will set your .Mac Sync Services back to square 1, meaning that 3rd party items will get removed (though your data in those apps will remain unscathed), and the next time you sync (I recommend performing one manually) you'll be asked all those 'brand new Mac' questions like "you are about to sync your calendars for the first time, do you want to merge, replace, etc."
Soon after you perform this reset, your 3rd party .Mac-aware apps *should* ping Sync Services to get on the list again, and I can personally say this worked for Yojimbo, but not Trasmit - yet. Ultimately, this might be a bit like using a sledgehammer to strike a nail, but it works - which is better than Apple's former solution of 'nothing.'