There were several variations for number 1, the application icon. You can build on those ideas or use one of them as is. You might want to have separate threads for each sub-type of icon (at least the application icon, because several pages can be spent making one sometimes).
Apel made some pretty attractive icons, but they won't suit your purposes. [link]
For section 3a and 3b: Do you really want to have an individual icon for each reference type only for the drag-and-drop cursor icon? Wouldn't a single icon for that be a lot easier? Or the text name of whatever's being dragged.
Other than those icon types (1. application icon, and 3a./3b. reference drag-and-drop icons) the other categories in your list were 2) modification status icons, which we've already discussed, perhaps we should focus on those, they should be easiest after number 1. The other categories were 4 and 5 and I don't think any work at all has been done with them yet.
A lot talk was passed back and forth about both Apel's icons and using Tango icons, neither of which solves anything for the task at hand, since like I said before Apel's stuff wouldn't be suitable and Tango icons were discussed for completely uninformed reasons (people thought you wanted toolbar icons already).