D: Highway 88/Carson Pass

This may be the most accessible High Sierra trailhead from the Bay Area, and it has some great trails. 
Like Desolation Wilderness, this gets a lot of traffic, so you can expect a few more regulations and quotas.  But there are also a number of hikes you can take that will see less traffic.  As always, aim for the middle of the week, or the off season, if you want to see fewer people.
We love this area for how quickly we can get there, and how beautiful the trails are, right from the start!  And over the years, this has become a great fall weekend destination for us.  

Showers Lake/Dardanelles Lake, and Round Lake
The premier destination here is probably Showers Lake, on the Pacific Crest Trail, but we actually preferred lesser known Dandanelles Lake.  These are all in the Tahoe National Forest, and are part of a possible new Wilderness Area:  Meiss Meadows.  We've heard that Round Lake has some nice cutthroat trout, but we didn't see any.  And the only fish we saw in Showers Lake were quite small. Still, this is a beautiful area that is also a great destination later in the year, when some of the high country is getting too darn cold.  Meiss Lake, in a swampy meadow, is also worth a visit if you don't mind getting your boots wet.  Really wet.  This photo on the left is Dardanelles Lake. 12 miles in a partial loop.
Lake Winnemucca and Round Top LakeAnother great destination along the Pacific Crest Trail, but these are only a couple of miles in, so they get a TON of traffic.  The trailhead at Woods Lake is quite lovely in and of itself, and then you get to climb up the slopes of Round Top Peak to these delightful lakes.  Camping is only allowed by reservations, and there are numbered campsites here, just like in a state park.  Not our idea of the perfect backpacking destination, but a great place for a quick getaway, particularly if you can do it in the middle of the week or on the shoulder seasons. This is Round Top Lake in mid-October, after the first snowfall of the season.  Only a couple of miles to either of these lakes/ 
You can also extend this trip to include a visit to Fourth of July Lake, further south, 14 miles rt. 
Granite Lake and Grouse Lake, out of the Blue Lakes trailhead east of Carson Pass:
A wonderful hike takes you past Granite Lake (Photo at left) out on top of a wild ridge, then across that ridge until you overlook Grouse Lake, about 1000 feet below.  Then you go down.  The total round trip is ten miles, and the scenery in the middle will simply take your breath away. (The photo at the top of the page is taken from this ridge.)   And this is a perfect hike for those days when the other trails are going to be packed with people.  There are not many fish in Grouse Lake, but Summit City Creek below the lake is supposed to have fish, and the canyon down there looks truly inaccessible and wild.  We went back a few years later to check it out.  See below!

Summit City Canyon:  This is another trail out of Upper Blue Lake (Evergreen Trailhead) that climbs for less than a mile and then descends
Summit City Canyon as we noted above.  The trail crosses Summit City Creek and then starts to follow the old Pioneer mining road down into Summit City, often straight down the canyon.  Past the junction to Fourth of July Lake, he trail gets very little traffic at all, and it is a lovely hike, following the creek, sometimes near, sometimes farther away, always within earshot.  And it goes for miles, all the way down to the Mokelumne River, and then beyond.  We haven't take it that far, and it may deteriorate into invisibility, but the section we hiked had been maintained in the last few years and was in good condition.  Expect to follow cairns and pay attention--this is definitely NOT the JMT freeway. And despite the isolation, the fishing is not great.  Small, skinny fish for the most part.  Here's a link to our trip blog from 2017: https://sites.google.com/site/backpackthesierra/home/our-blog/beatingtheheatbeatingthecrowds
Lake Margaret:  This is an easy 2.5 mile hike down from the pass into the Tahoe National Forest.  The lake will get a lot of dayhikers, but it's quiet in the morning and evening, and there are some fish in the lake.  The creek on the way is so beautiful that many dayhikers get distracted and never make it to the lake!  It's also a good one for early or later in the year, as the elevation is a good 1000 feet lower than any of the others on this page.