Since Milestones are only one level, it may make sense to have a "Milestone" tag that is [ Project > Milestone ]
I think this is actually a little tricky. In the UI, I'd like to see us auto pre-pend the Project Name with the Milestone, then represent that as the object everywhere (search, tags, typeahead, page title). But that likely means using some UTF-8 delimiter over a pretty pretty icon.
This bare "v3" in the is still a little weird:
..but I figure we'll eventually replace it with a beefier element, at least in non-collapsed mode, when this fancy stuff gets some kind of work done on it:
I really like the look of the inverse tag, although I haven't personally felt too much confusion about milestones vs nonmilestones on project pages.
Shy of inverting the tags, the fatter menu header might help with that -- we could also consider making that provide a stronger callout for milestones vs projects.