Is Automator suitable for complex folder based workflows?
There is a similar workflow kit at http://forums.macrumors.com/showthread.php?t=805573 that takes disc images (dvd, bluray, etc.) and converts them to various formats.  There are a number of actions you could copy for file movement, etc., and attach them as folder actions to A, B, and C.

It should also be a simple matter to pick and choose which actions and workflows you would require for this.

Even better, the underlying technology for these actions are just shell scripts.  If you can write a shell, ruby, python, etc. script, you can create your own Automator action.  You could easily store state regarding files in A, B, and C that have already been copied to D and only copy them again if certain criteria are met, such as a change in file size, modify date, or md5 hash.