September/October mean very small waterfalls, and not very many waterfalls. Weekends are still crowded though not as bad as July/August. Usually all parts of the park are accessible by vehicle, though storms can result in temporary closures, and October is less dependable road wise than September. Great hiking is usually still available throughout most of the park. Avoid Labor Day weekend, the first weekend in September. Leaves in Yosemite Valley generally don’t start changing color until the end of October, but this is hugely variable. Also, the color change isn’t as dramatic as the western parts of the United States. Aspens in the higher elevations can start changing over in middle to late October as well. Just remember that Tioga Road can experience temporary (sometimes multi day) closures throughout October if cold storms roll in.
To see waterfalls at their best, visit in late May to early June. Snowpack in the higher elevations will be melting, meaning waterfalls in Yosemite Valley and Hetch Hetchy will be close to peak. When exactly the true peak occurs varies from year to year based on weather. However, visiting anytime during this window can pretty much guarantee impressive water. These are also the good months for moonbow viewing during full moon time periods. Mirror Lake is largest at this point. There are disadvantages to this time period. Particularly in late May, but even into June, Glacier Point Road and particularly Tioga Roads may still be closed. Again, this depends on the weather and the snowfall of the preceding winter. It is key to have alternate plans if coming to Yosemite from the eastern side of the Sierra Nevada (Las Vegas, Reno, Death Valley). Also, even if Glacier Point Road and Tioga Road are open, some hiking trails may still be very difficult to find as they may still be covered in snow. This particularly applies to trails off of Tioga Road, but can also apply to Glacier Point Road. Again, flexibility in high elevation hiking plans is key during this time. Remember that Yosemite Falls is frequently dry any time from late July to late August (and into September), with other waterfalls diminishing significantly as well during this time.
To see as much of the park as possible by car, July through September will be the time to visit. Fairly consistently (though there are exceptions) all of the roads are open during these months. Both the lower and higher elevation areas of the park are generally accessible, with at least some, if not a ton, of hiking available. July 2011 saw some hiking still restricted by snow and very, very high water. However, this was an unusual year with lots of more snow than usual. July and August tend to be the busiest months of the year. If possible, avoid the park on Saturdays and Sundays. Weekdays are also very crowded, but traffic tends to peak on the weekends.