When everyone talks about Shawn's last run, they always talk about the "Vices" storyline or his feud with D-Bry, and those were both good, but the one that I'll always remember is how he saved the Nexus from being completely tanked as a stable. I remember reading The Life and Times of the American Dragon the autobiography D-Bry put out after his retirement (still a shame he had to retire) and he talks about how part of the plan for the "NXT Riot" as WWE had since dubbed it was for him to go out and choke out Justin Roberts with his own tie, but Shawn had talked him out of the spot and suggested they go with a different spot. That's how we got that awesome spot where HBK (who was in the midst of his feud with Punk at the time, if memory serves me right) had run out to try and make the save, only to get jumped by Daniel and put in a LeBell Lock and held him off from helping Punk or Cena.
Bryan himself says that the changed spot saved his career since the tie-choking would've gotten him fired and without the second in command of the Nexus (and World Heavy Champion of the stable) the group would've struggled. Plus, HBK took the fall for D-Bry to give the Nexus the victory at SummerSlam 2010, which helped solidify D-Bry as a future star in the company. And without that momentum, we would've had the D-Bry vs. Kaval match, a match Meltzer rated five stars (not seen since HBK-Undertaker in 1997) that helped save Kaval's career in the WWE. While Kaval himself didn't win the title or hold the world title for any amount of time, the match did give him the momentum to be booked to win the IC title off Justin Gabriel at the start of 2011 and began his really good year-long IC title run.
I could keep going, but I think just saving two indy stars' careers and keeping a really hot storyline from fizzling out are some really good highlights from Shawn's final run.