The John Muir Trail is a famous 357 km trail that runs from Yosemite
to Mt Whitney (Whitney Portal).
It is not a favorite of mine: it misses most of the great natural wonders of California. It was built to connect point A to point B, not to provide an overview of California's best places. Thus it misses Darwin Canyon, the Sphinx lakes, Shepherd Pass, the Palisades, Bishop Pass, and of course all the great summits of the Eastern Sierra except for Whitney. In Yosemite it misses both Half Dome and Clouds Rest. The highlights of the trail (such as the Rae Lakes) are mostly reachable with day hikes. The notable exception is Evolution Lake. It is also a very crowded trail. On a day in july 2009 we literally met people every 15 minutes. A far cry from what i call "wilderness".
The trail crosses these major passes: Donohue Pass (but misses Mt Lyell), Muir Pass, Mather Pass, Pinchot Pass, Glen Pass (great views of Rae Lakes, but misses the Sixty-lake Basin), Forester Pass (the highest pass at 4,009 m).
Notes of 2007:
Pictures of the main sections that i have hiked: