Phase III changed the handling of free-standing URLs: if the last letter of the URL is a period, comma, semicolon or parenthesis, it is taken to be part of the URL. I think this should be changed back to the Phase II behavior.
I entered this before as a feature request, and I just learned that Brion also favors the change. Lee argues that the current behavior is correct.
I say that the goal is not formal correctness, but user satisfaction. URLs almost never end in one of these special symbols, but when used as part of Enlish sentences, they are often followed by one of them. Numerous links all over Wikipedia have been broken by this change. Just one example: http://www.wikipedia.org/wiki/BryceHarrington.
Axel