I haven't tried to plan a trip on 511.org
in a while, and I just realized that it has a funny limitation. If you ask it for the latest trip for today, it doesn't have a flexible enough concept of 'today' to include trips that involve taking a transit vehicle that departs after midnight, i.e., tomorrow. So when I ask it for the latest trip, it excludes the ability to take the 12:01am Caltrain of the Damned, which rather perplexes things because without that option, for the trip in question, I would have to leave earlier than I arrive.
I'm pretty sure it does allow you to take a trip that involves arriving tomorrow, just not one that also involves departing tomorrow. However, it is helpful enough to tell you what the later trips for a particular leg are, so it's not too hard to get from there to figuring out when you actually need to leave.