We've instrumented the version of Mono that Unity v4.6 uses so it can create a full heap transaction log, as well as full heap memory snapshots after all GC's. With this data we can build complete graphs of all objects on the Mono heap, either going "down" starting from the static roots, or "up" from a single object. Note this heap visualization method is relevant to C/C++ too, because at its core this version of Mono actually uses the Boehm Collector for C/C++.
To build this graph, we recorded a heap transaction log and post-GC memory snapshots of our product running a single dungeon and exiting to the game's menu. I then played back this transaction log with our analysis tool ("HeapBoss") and stopped playing back the log right after the dungeon was exited. I had the tool start building the graph at a single ScriptableUXObject object on the heap (instances of this type are leaking after each dungeon). The tool then found all references to this object recursively, up to any roots and exported the graph to a .dot file. Gephi is used to visualize the graph, using the Yifan Hu algorithm to optimize the layout.
Using this visualization method we quickly determined why these objects are leaking, which was easy once we could visualize the chain of references in various containers back up to the UXManager.