I haven't watched Free! yet, but it's slice-of-life about a swim team full of eyecandy dudes, yeah? So I guess a character who was way better than any of the main characters at swimming, and whose presence threw any or all of their personalities out of whack in order to fulfill some shipping fantasy or other would be a couple of qualifiers. Or perhaps there's an OC who really likes boys who play basketball, so one of the dudes (like, say, Haruka Nanasae, who according to MAL "always loved to be immersed in water, and to swim in it") give up swimming to join the basketball club impress the character, that OC is prooobably a Sue.

Basically, just take whatever makes Free! what it is, and add a character who turns that on its head for no good reason. I wish I knew more about the show, so I could have a more informed opinion XD

Mary-Sues are pretty much the same in all continuum.
Unless you're implying that all of the characters in the canon of Free! fit the normal definition of Sues/Stus, they should still be the same as a normal Sue.