I was looking for ways to get to Yosemite without driving myself, and came across Extranomical Tours. I booked with them directly and managed to arrange a 2-night stay at the Yosemite Valley Lodge. They were responsive over email and the booking process was relatively fuss free.
I was picked up at the Hilton Union Square along with other tour group members, most of them on day trip and a few others staying overnight... for my particular departure they sent 3 buses for pick up so u had to wait for your name to be called before getting onto the bus. A little nerve wrecking to be one of the last ones called, but all good in the end.
It's semi-guided because the guide (who's also the driver) does not go with you the whole way at the sight seeing stops... we were dropped off at the sight seeing points, given an introduction and instructions for when to return, and then the time is free for you to do what you want, whether it's to walk or sit down for a picnic. If you are staying overnight, the bus drops you off at the Valley Lodge (with the day trippers) and you're free to spend the rest of the time as you please... in my case I had a good wander around the lower valley floor after checking in, went on a guided hike with another tour company on the second day, and took the tram tour on the morning of the third day. On the afternoon of the third day I called ahead to confirm the departure time, and duly got on the bus back to San Francisco without incident.
Denise was the driver and guide for my trip there and back, and I found her to be professional and an excellent driver. The buses I was on were in good condition, and I liked that it's smaller than the big tour buses.
I was slightly nervous about this operator as some reviews were less than stellar, but for me everything worked out smoothly and I had a great time in Yosemite. It definitely warrants more than a day trip!
One thing I would suggest for improvement is they could cater a bit better for visitors who don't understand English... for my group there were quite a few of them and none had headphones (which were supposed to be provided) to listen to the commentary... and ended up looking a little lost most of the time.