Well, if we're talking over a really substantial period of time, Djokovic in 2011 stands out, as does Federer in 2006. Those are two players who were in the zone for pretty much entire year, minus some stretches.
Nadal's stretch from Hamburg 2008 till the Olympics later that year was probably the best tennis of his career. 2010 was interesting, because while it was his best year to date, his results were superb, but his level wasn't always "in the zone" (save for maybe the best tournament of his career at Monte Carlo). However, at the US Open that year he was something else. When one of your weakest shots clicks so much (the serve), you are in the zone.
The most recent example of someone being in the zone for more than just a tournament is Nadal himself, last summer on North American hard courts. He hardly broke a sweat with the exception of the Djokovic match in Montreal.
I do think Nalbandian's fall of 2007 is worth mentioning. He was playing otherworldly tennis that unfortunately sentenced us to years of torment and arguments on these boards.
IF we narrow down "the zone" to one match, then there are plenty of examples, because literally any player can get in the zone. Tsonga vs Nadal at the AO in 2008 or Kyrgios vs. Nadal at Wimbledon this year are good examples. Both were unknowns at the time when those matches took place, and nobody even knew they had that level in them. This is different to top players being in the zone because, as good as they play, we're never really THAT surprised.
It's weird when unexpected players get in the zone for an entire tournament though. Cilic is obviously the most recent example. But I'd even cite a few examples that have long been forgotten: Mardy Fish at the 2008 Indian Wells, or Ljubicic at the same tournament two years later. It's not that they just won the tournament out of nowhere, but the level of play they displayed was really surprising, especially because they'd both been on tour forever and we'd never seen anything like that (in fairness to Ljubicic, he was a top 3 player at one point, but rarely put it together like that for an entire tournament, not to mention the fact that he did it so late in his career).
Anyway, I limited this to relatively recent examples otherwise this post would take pages.