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I know the @username isn't technically a markdown format, but I had no idea that using it actually notified people in the comments of a reply until I got reprimanded for it.
I originally thought it was just a twitter-ism. But twitter highlights it, yes? Shouldn't people be keyed in to the idea that @ actually does something by making blue, or linking to the user's profile?
Thanks,
I don't find highlighting to be a wise idea, largely because comment replies are not a visually taught system. I enumerate in this answer why highlighting isn't going to be particularly useful to the recipient; there are enough notifications attached to comment replies that highlighting is entirely unnecessary. So let's focus on the faults of highlighting as a teaching system.
To the point: comment replies are too complex to teach by demonstration alone. Knowing the rules behind them is necessary to their proper utility, otherwise you only propogate mis-usage, and no one learns anything.
As I spoke of in this answer, there are a lot of different quirks to the comment reply system. Between the short-hands, the white-space issue, and the fact only one comment reply can work, it is not very easy to understand what works and what doesn't. The fact that no one repairs broken replies (often because it's well after 5 minutes) means there's a lot of mis-information on the system prevalent throughout the sites. People even use @ to try and reply to downvoters, or to also refer to people who aren't even in the conversation string.
Introduce highlighting into the mix and you don't get any good comprehension out of users. If we restrict the highlighting to only when it was successful, it won't always make sense. For the most ludicrous case, consider the comment exchange on this answer: that @devinb isn't a successful comment reply because at the time, devinb had a nulled username. When you add users who change name (myself as a prime example) and users who are in the middle of an edit revision history, what you get is a lot of confusion as to what is a legal reply and what isn't. Highlighting is not really doing to improve that comprehension because two otherwise matching mentions can be unmatched in highlighting in the same comment stream.
