I find the Night Owl service of MUNI (route 90) to be particularly good. It gets you from Union Square to Cow Palace in 40 minutes, and you don't have to deal with parking at all. You just board in your cycling gear and with your single piece of luggage at hand, and you get dropped off at the end of the line (which means you can safely sleep on board).

Once you get in, you can check-in with your bike. I recommend going back and checking tire pressure, since later it becomes highly stressful. Knowing where your bike is makes it much easier to find it once you get going, too.

Next, the Opening Ceremony. I confess I find the spectacle particularly lame, especially because participation is enforced and the speakers not so exciting. Still, a good chance to connect with people.

After that's over, you walk to your bike, put on the helmet, and leave. Watch out, since many of the cyclists around you aren't too comfortable on their bikes at the early hour - if there is a crash, it's more likely to happen in the first tenth of a mile than during the rest of the day (the FDA didn't evaluate this statement).