After Labor Day (first Monday in Sept.) it should be uncrowded. It's starting to cool down, especially in the high country (Tioga Road).
I don't know what's still running. There's a tour bus from Yosemite Valley to Glacier Point that runs in the morning. See
http://www.yosemitepark.com/ for details. Then you can walk down the trail. If the bus is not running, you have to walk up and down, making it basically a full day (unless you leave early or rush). Walking down is easy, unless you have knee problems. Walking up and down is not hard--it's a nice trail, but you need to be in reasonable shape.
Glacier Point is a terrific view of Yosemite Valley (and Little Yosemite Valley). If you have limited time, you can just drive to Glacier Point.
There's also the Giant Sequoias groves. The best is the Mariposa Grove at the southern end of the park. The tour busses are probably not running then, but you can walk. Another full day. There are two other smaller Sequoia groves north of Yosemite Valley that are easier to reach.
Then there's the classical falls in the Valley--Bridal Veil, Yosemite, Vernal, and Nevada. Plenty to see and do.