This is another poll where I really enjoyed both runs, but to me, the clear winner is Sinestro Corps Wars. Flashpoint is a really good story (probably my favorite Flash story, though to be fair, I haven't read too many), and it had some amazing art by Kubert, but it relied pretty heavily on some of the tie-in comics to fill in the blanks for the readers, and a lot of those tie-ins weren't nearly as well written as the main series (though I did love Azzarello's Batman tie-in and Scott Snyder's Superman tie-in). The animated movie, The Flashpoint Paradox, did a much better job of presenting a much more cohesive storyline, and the story was better for it.
The main story of Sinestro Corps Wars was pretty well contained in the main two GL books at the time (GL and GL Corps), and it is probably one of the best, if not the best GL stories I've ever read (which unlike Flash, I have read my fair share of GL stories). It is epic in scale, and the central conflict revolves around the relationship between Hal Jordan and Sinestro, which to me, is one of the most interesting relationships in comics (somewhat similar to Xavier and Magneto's relationship, in that they used to be friends but are now bitter rivals,, though they still have a begrudging respect for one another). It also shows Hal's continuing struggles to regain the trust of the other Lanterns again, and his efforts to bring people (and, in a broader sense, hope) back to Coast City. I also loved the scene where Hal and Kyle were running across the rooftops, trying to get away from Sinestro without the help of their rings. That was a pretty awesome scene. And the art throughout the story (in both GL and GL: Corps) is amazing.
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.