Well I think those are Scott Snyder's two best Batman stories so far (though I haven't read Zero Year yet, so maybe it blows these other two out of the water), but I think I have to give a slight edge to The Black Mirror. That book was extremely creepy and suspenseful, and was really just about perfect. Death of the Family is one of the best Joker stories that I have read, but it just doesn't quite reach the same level of quality that Black Mirror did. Regardless, two great Batman stories by one of my favorite comic book writers.
I just finished re-reading what I have of Excalibur after I got a bunch of issues that I had been missing from my collection. Chris Claremont's run for the first 30 or so issues and Warren Ellis' run near the end of the series are by far the best issues. Very fun stories by those writers. The rest tends to range from meh to pretty good.
I just recently got a bunch of issues from Claremont's run on Uncanny X-Men (Essential X-Men vol 5, which contains issues 180-198), so I'll probably be going back to re-read what I already had of that amazing run as well.
Year One, No Man's Land, Watchmen, Killing Joke, The Dark Knight Returns, The Black Mirror, For the Man Who Has Everything, Whatever Happened to the Man of Tomorrow, All-Star Superman, Long Halloween, Joss Whedon's, Grant Morrison's, and what I've read of Chris Claremont's respective X-Men runs, Ultimate Spider-Man... just to name a few. Couldn't choose just one...
Both are fantastic stories. Batman RIP is a trippy, complex, well thought out story that features a thrilling showdown between Batman and the Joker, as well as with the Black Glove, who had, up to that point, been plaguing Batman throughout Grant Morrison's run. It also introduced some of the campier Batman stories from the 60s into modern continuity in a pretty cool way. It is a very good Batman story that is easily one of the 20 or 25 best Batman stories written (out of the ones that I've read thus far, anyway).
I voted for All-Star Superman though, because it is one of three Superman stories that I'd put at the top of my "Best Superman Stories" list (the other two being "For the Man Who Has Everything" and "Whatever Happened to the Man of Tomorrow," both by Alan Moore). Grant Morrison just really gets Superman's character. He is a powerful being, who also happens to be very caring and, because of that, always tries to put humanities needs before his own. A lot of times Superman is simply written as a two-dimensional boy scout that often solves everything with punches or super breath. Grant Morrison's story really fleshes out the character of Superman, and shows how interesting a character like Superman can be. Not to mention his supporting cast. I've never seen a cooler incarnation of Jimmy Olsen.
Easily the Wolverine mini series by Chris Claremont and Frank Miller. After that I'd say the first 20 or so issues of Wolverine's first ongoing series, then Larry Hama's run on Wolverine, Greg Rucka's run, Wolverine and Kitty Pryde, and then Mark Millar's run.
I also really enjoyed Whedon's portrayal of him and his appearances in the X Force books he's been in, but I would agree with someone else that said those aren't really Wolverine stories so much as they are X-Men (or X-Force) stories.