Let's settle this once and for all. I personally have witnessed my gold (or, at least, some of it) being marked as stolen in my inventory in the past. I've seen several comments around here from people who claim the same. Though none of us can yet explain it, I believe there's no longer any point in arguing that it does happen.
Also, if you'll pardon the quality, I do have an image to share of one of my current characters' gold in the inventory screen. I still don't know how this happened, but this does demonstrate that at least some of her gold is in fact marked Stolen. This was taken with my camera-phone.
However, some people still claim that gold cannot be flagged as stolen property. They even cite the venerable UESP as a source for this: "Gold is considered completely fungible in-game, and will never be marked stolen, or confiscated if you are apprehended by the guard."
So, I'd like us to settle this here now. For anyone with the time and will to play-test this, please document your findings here. I'm going to post mine below. I've not been able to reproduce the phenomenon so far, but I'm not inclined to give up because I know it can happen.
P.S.: If anyone's got a clue as to what may be causing this, but has not play-tested it yet, please feel free to mention your ideas in comments.
P.P.S: For the record, after I decided to take a break from play-testing this, I loaded up one of my other characters to play for awhile and found that she currently has some stolen gold on her. How much of the gold is actually marked stolen, I'm not inclined to figure out right now. Dropping small bits from a stack of more than 100,000 isn't exactly a user-friendly process on the PS3.
P.P.P.S: Since the comment-discussions here have gotten a bit long I've created a Skyrim Play-Testing chat room, where we can continue working on this issue without further bloating this thread. If you do participate there, please make sure that any details which may be relevant to future readers of this thread get posted to the Q&A or comments here.