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Stephen,
Since I have used UR for about three weeks, so far I haven't run into the need to link documents much with each other (if, by documents, you mean included/linked files of the Office/PDF variety). But I'm sure I will use this in the future.
Let's imagine I am writing a proposal. Each draft of the proposal could be a document and also have as children links to other documents that I refer to when building the proposal (spreadsheets, etc.). Each item, whether a document or otherwise, can "live" with the other items it relates to, one or many times.
I may have misunderstood your point if you are referring to documents in a more general sense (any written text item). If you intended this more expansive meaning of document, then I do link these together quite freely.
The only trouble I have with the basic approach of linking manually is that I must remember what sort of structures I am trying to build. Saved search items relieve some of this burden. Still, manual linking is not quite to the level of "assignment" in Zoot, where you build in some initial structure and then it's very easy to "link" items to certain concepts without needing to navigate around a tree.
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